diff --git a/modules.json b/modules.json index bf7045d4..bd712cb4 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["bam_variant_calling_mpileup_bcftools"] }, "bcftools/concat": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["vcf_gather_bcftools"] }, "bcftools/convert": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["modules"] }, "bcftools/index": { @@ -36,42 +36,42 @@ }, "bcftools/merge": { "branch": "master", - "git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["bam_variant_calling_mpileup_bcftools"] }, "bcftools/mpileup": { "branch": "master", - "git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["bam_variant_calling_mpileup_bcftools"] }, "bcftools/norm": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["modules"] }, "bcftools/pluginsplit": { "branch": "master", - "git_sha": "440edf75d8782913115a7b72a88392a227f72cc1", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["modules"] }, "bcftools/query": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["vcf_gather_bcftools"] }, "bcftools/stats": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["modules", "vcf_impute_beagle5"] }, "beagle5/beagle": { @@ -128,7 +128,7 @@ }, "glimpse2/phase": { "branch": "master", - "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", + "git_sha": "2057a0a8dbd67000d08613a556570aa7184a7c89", "installed_by": ["bam_vcf_impute_glimpse2", "modules"] }, "glimpse2/splitreference": { @@ -153,12 +153,12 @@ }, "multiqc": { "branch": "master", - "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36", + "git_sha": "79b36b51048048374b642289bfe9e591ef56fe05", "installed_by": ["modules"] }, "quilt/quilt": { "branch": "master", - "git_sha": "4e2990cc0df18823d11b192df73039c80fdebc7c", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["bam_impute_quilt", "modules"] }, "quilt/quilt2": { @@ -168,42 +168,42 @@ }, "samtools/coverage": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", "installed_by": ["modules"] }, "samtools/depth": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", "installed_by": ["bam_subsampledepth_samtools", "modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "44b7dad0181c7a0495f6d128d8cbf55feb277a84", + "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", "installed_by": ["modules"] }, "samtools/reheader": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", "installed_by": ["modules"] }, "samtools/view": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "2057a0a8dbd67000d08613a556570aa7184a7c89", "installed_by": ["bam_subsampledepth_samtools", "modules"] }, "shapeit5/ligate": { "branch": "master", - "git_sha": "236d7f19efcffccdfac5e1850af2aa035e0de79c", + "git_sha": "25ac0da595fac900aba3041d2bcdd7eb338192d0", "installed_by": ["modules", "vcf_phase_shapeit5"] }, "shapeit5/phasecommon": { @@ -237,7 +237,7 @@ "nf-core": { "bam_impute_quilt": { "branch": "master", - "git_sha": "4e2990cc0df18823d11b192df73039c80fdebc7c", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["subworkflows"] }, "bam_impute_quilt2": { @@ -247,17 +247,17 @@ }, "bam_impute_stitch": { "branch": "master", - "git_sha": "e1cb31f0ced0d0810d1cb099aaa690b05beb1f3a", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["subworkflows"] }, "bam_subsampledepth_samtools": { "branch": "master", - "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338", + "git_sha": "2057a0a8dbd67000d08613a556570aa7184a7c89", "installed_by": ["subworkflows"] }, "bam_variant_calling_mpileup_bcftools": { "branch": "master", - "git_sha": "fedf60f97f2dc2251f7d2d1cf83c93b001f5b2f7", + "git_sha": "4b21e2cd1a9ea70e22b502cb45ee147410824760", "installed_by": ["subworkflows"] }, "bam_vcf_impute_glimpse2": { @@ -272,12 +272,12 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", + "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", + "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", "installed_by": ["subworkflows"] }, "vcf_gather_bcftools": { @@ -302,7 +302,7 @@ }, "vcf_phase_shapeit5": { "branch": "master", - "git_sha": "236d7f19efcffccdfac5e1850af2aa035e0de79c", + "git_sha": "25ac0da595fac900aba3041d2bcdd7eb338192d0", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 18778cc2..c12bd7a7 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_ANNOTATE { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(columns), path(header_lines), path(rename_chrs) diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index 10af196a..91fca741 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -27,16 +27,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:54:34.686330171", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:29:19.618749659" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": { "content": [ @@ -66,16 +66,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:53:48.564151048", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:43.350060834" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": { "content": [ @@ -105,16 +105,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:53:38.715013376", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:36.101003418" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": { "content": [ @@ -144,16 +144,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:54:52.117082881", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:29:34.19449127" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": { "content": [ @@ -183,16 +183,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:54:43.025430475", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:29:26.927815399" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": { "content": [ @@ -222,16 +222,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:53:29.538130871", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:28.891823681" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": { "content": [ @@ -255,16 +255,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:54:25.811513664", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:29:12.400301681" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output": { "content": [ @@ -288,16 +288,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:53:58.362749653", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:50.375384421" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ @@ -321,16 +321,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:53:20.809593889", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:21.320211288" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ @@ -354,16 +354,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:53:13.16941797", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:13.274072987" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": { "content": [ @@ -393,16 +393,16 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:54:16.229056032", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:29:05.094685409" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output": { "content": [ @@ -426,15 +426,15 @@ [ "BCFTOOLS_ANNOTATE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:54:07.560097761", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-27T15:28:57.906382655" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 269da8e0..c9d63d47 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_CONCAT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 5edf5beb..d50df8c3 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -25,16 +25,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:56:40.943674504", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T11:59:52.705734505" + } }, "homo_sapiens - [[vcf1, vcf2], []]": { "content": [ @@ -57,7 +57,7 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -78,16 +78,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:58:37.284385652", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:00:08.498123366" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ @@ -110,7 +110,7 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -131,16 +131,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:58:46.526849891", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:00:15.986212097" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { "content": [ @@ -168,7 +168,7 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -194,16 +194,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:58:54.955073113", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:00:24.007593166" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { "content": [ @@ -231,16 +231,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:57:21.150275043", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:00:00.937832062" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ @@ -263,7 +263,7 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -284,16 +284,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:56:22.417694939", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T11:59:37.378838683" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { "content": [ @@ -321,16 +321,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:56:32.059807083", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T11:59:45.296771646" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { "content": [ @@ -358,7 +358,7 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -384,16 +384,16 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:59:15.441351979", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:00:39.792930532" + } }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { "content": [ @@ -421,7 +421,7 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -447,15 +447,15 @@ [ "BCFTOOLS_CONCAT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:59:05.703998433", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:00:31.985353981" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/convert/environment.yml b/modules/nf-core/bcftools/convert/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/convert/environment.yml +++ b/modules/nf-core/bcftools/convert/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index 05ae8e22..100276dd 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_CONVERT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/convert/tests/main.nf.test.snap b/modules/nf-core/bcftools/convert/tests/main.nf.test.snap index 71f78f59..2245447a 100644 --- a/modules/nf-core/bcftools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/convert/tests/main.nf.test.snap @@ -17,16 +17,16 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T17:59:53.631512862", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:01:10.83392125" + } }, "homo_sapiens - vcf1, tbi, [], fasta - to hap": { "content": [ @@ -59,16 +59,16 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:00:03.621869785", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:01:18.182232629" + } }, "homo_sapiens - vcf1, tbi, [], fasta - to hap - stub": { "content": [ @@ -119,7 +119,7 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ], "bcf": [ @@ -168,16 +168,16 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:00:32.196885655", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:01:40.91416397" + } }, "homo_sapiens - vcf1, tbi, bed, fasta - to gvcf - stub": { "content": [ @@ -223,7 +223,7 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ], "bcf": [ @@ -267,16 +267,16 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:00:40.858193336", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:01:48.165685025" + } }, "homo_sapiens - vcf1, tbi, [], fasta - to bcf - stub": { "content": [ @@ -322,7 +322,7 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ], "bcf": [ @@ -366,16 +366,16 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:00:23.094047342", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:01:33.611498588" + } }, "homo_sapiens - vcf1, tbi, bed, fasta - to gvcf": { "content": [ @@ -395,15 +395,15 @@ [ "BCFTOOLS_CONVERT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:00:13.635216768", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:01:25.786789989" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/merge/environment.yml +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index f1acbd3d..644565ce 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcfs), path(tbis), path(bed) diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap index 9dd09178..26f357c8 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap @@ -8,16 +8,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:45.080843391", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:01.453191274" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub": { "content": [ @@ -37,7 +37,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -55,16 +55,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:25.25403025", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:43.064165277" + } }, "sarscov2 - [vcf, tbi], [], [], bed": { "content": [ @@ -74,16 +74,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:52.858929503", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:09.906419282" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub": { "content": [ @@ -108,7 +108,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -131,16 +131,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:56.583006641", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:06:17.06290054" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf output": { "content": [ @@ -150,16 +150,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:03:57.570236761", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:14.044948834" + } }, "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub": { "content": [ @@ -179,7 +179,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -197,16 +197,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:48.75796761", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:06:08.633006073" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub": { "content": [ @@ -231,7 +231,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -254,16 +254,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:06:11.006590962", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:06:33.897407991" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub": { "content": [ @@ -283,7 +283,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -301,16 +301,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:33.181550902", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:51.445673109" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index": { "content": [ @@ -321,16 +321,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:37.289045617", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:53.868676326" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output": { "content": [ @@ -340,16 +340,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:05.940999977", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:22.660557224" + } }, "sarscov2 - [vcf, tbi], [], [], [] - bcf output": { "content": [ @@ -359,16 +359,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:13.622386289", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:30.965022315" + } }, "sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub": { "content": [ @@ -388,7 +388,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -406,16 +406,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:41.084610701", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:59.932077434" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index": { "content": [ @@ -426,16 +426,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:29.469178039", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:46.41923299" + } }, "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output": { "content": [ @@ -445,16 +445,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:01.918013292", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:18.989455751" + } }, "sarscov2 - [vcf, tbi], [], [], [] - one sample": { "content": [ @@ -464,16 +464,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:09.444730199", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:26.431607458" + } }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ @@ -493,7 +493,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -511,16 +511,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:05:16.820762299", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:05:34.692613749" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub": { "content": [ @@ -545,7 +545,7 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ], "index": [ @@ -568,16 +568,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:06:03.842949519", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:06:25.137261969" + } }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -587,16 +587,16 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:03:49.803735629", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:05.637837157" + } }, "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output": { "content": [ @@ -606,15 +606,15 @@ [ "BCFTOOLS_MERGE", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:04:20.850645013", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:04:38.467108836" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml index cb55500b..ee5cb56d 100644 --- a/modules/nf-core/bcftools/mpileup/environment.yml +++ b/modules/nf-core/bcftools/mpileup/environment.yml @@ -5,5 +5,5 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::bcftools=1.22 - - bioconda::htslib=1.22.1 + - bioconda::bcftools=1.23.1 + - bioconda::htslib=1.23.1 diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index 0b35ddac..cd46bde0 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_MPILEUP { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(bam), path(intervals_mpileup, stageAs: 'mpileup_intervals/*'), path(intervals_call, stageAs: 'call_intervals/*') diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap index b7091f99..9cb64afe 100644 --- a/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap @@ -8,7 +8,7 @@ { "id": "test" }, - "test.bcftools_stats.txt:md5,a3ed9abd409e4aa435f85924e4d0bad4" + "test.bcftools_stats.txt:md5,de12663777205adcf4eb290f51785507" ] ], [ @@ -16,7 +16,7 @@ { "id": "test" }, - "test.mpileup.gz:md5,86f0f5fcaba16e1b4af035ff2b5a9bf3" + "test.mpileup.gz:md5,0bf4906ac9abc7f65e84117aea1869ec" ] ], { @@ -24,14 +24,14 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2025-12-21T14:06:18.298267588", + "timestamp": "2026-03-20T18:06:34.052916869", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" } }, @@ -74,7 +74,7 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ], "mpileup": [ @@ -113,14 +113,14 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2025-12-22T09:01:23.428267089", + "timestamp": "2026-03-20T18:06:26.164134401", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" } }, @@ -133,7 +133,7 @@ { "id": "test" }, - "test.bcftools_stats.txt:md5,ddfe3704ece40c8d3b8a8beb31cfbcf9" + "test.bcftools_stats.txt:md5,71b0ba767e62d6d4465383c1f3aefec6" ] ], { @@ -141,15 +141,15 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-02T13:20:19.914560249", + "timestamp": "2026-03-20T18:06:48.873015944", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "sarscov2 - [bam, []], fasta, true stub": { @@ -191,7 +191,7 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ], "mpileup": [ @@ -230,14 +230,14 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2025-12-22T09:01:37.014405367", + "timestamp": "2026-03-20T18:06:41.070206975", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" } }, @@ -250,7 +250,7 @@ { "id": "test" }, - "test.bcftools_stats.txt:md5,163481111816620f6b76a5e96976e93a" + "test.bcftools_stats.txt:md5,97b0f9e01ecd7c4e39d6ef799de496cb" ] ], { @@ -258,15 +258,15 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-02T13:20:37.262876642", + "timestamp": "2026-03-20T18:07:06.024890778", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "sarscov2 - [bam, bed_call], fasta, false": { @@ -278,7 +278,7 @@ { "id": "test" }, - "test.bcftools_stats.txt:md5,6ae3528d5393335f19135bd0e39f80e8" + "test.bcftools_stats.txt:md5,5dfd90826a0228d35e9630bd1335e875" ] ], { @@ -286,15 +286,15 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-02-27T17:05:45.469300576", + "timestamp": "2026-03-20T18:06:57.781993923", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.2" } }, "sarscov2 - [bam, []], fasta, false": { @@ -306,7 +306,7 @@ { "id": "test" }, - "test.bcftools_stats.txt:md5,a3ed9abd409e4aa435f85924e4d0bad4" + "test.bcftools_stats.txt:md5,de12663777205adcf4eb290f51785507" ] ], { @@ -314,14 +314,14 @@ [ "BCFTOOLS_MPILEUP", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2025-12-21T14:06:04.63975552", + "timestamp": "2026-03-20T18:06:18.776255025", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" } } diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 443c8bbb..ddc7e2d1 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_NORM { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap index ee2dadf7..07b4dfc4 100644 --- a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap @@ -20,7 +20,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -41,16 +41,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:44.337029292", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:29.987030961" + } }, "sarscov2 - [ vcf, [] ], fasta - stub": { "content": [ @@ -73,7 +73,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -94,16 +94,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:21.46950981", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:06.488086505" + } }, "sarscov2 - [ vcf, tbi ], fasta - vcf output": { "content": [ @@ -126,7 +126,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -147,16 +147,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:07:50.103984525", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:08:34.863776359" + } }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub": { "content": [ @@ -184,7 +184,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -210,16 +210,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:09:07.527342293", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:54.718705045" + } }, "sarscov2 - [ vcf, tbi ], fasta - vcf_gz output": { "content": [ @@ -242,16 +242,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:07:57.732501354", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:08:43.007377633" + } }, "sarscov2 - [ vcf, [] ], fasta": { "content": [ @@ -274,7 +274,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -295,16 +295,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:07:13.798479336", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:07:54.877084219" + } }, "sarscov2 - [ vcf, tbi ], fasta - vcf output -stub": { "content": [ @@ -327,7 +327,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -348,16 +348,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:36.850690402", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:22.220435939" + } }, "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output": { "content": [ @@ -380,7 +380,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -401,16 +401,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:13.766769548", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:08:58.483532889" + } }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub": { "content": [ @@ -438,7 +438,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -464,16 +464,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:09:14.639868288", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:10:03.22576704" + } }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi": { "content": [ @@ -489,11 +489,11 @@ ] ], + "timestamp": "2024-06-05T13:53:28.356741947", "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" - }, - "timestamp": "2024-06-05T13:53:28.356741947" + } }, "sarscov2 - [ vcf, tbi ], fasta": { "content": [ @@ -516,7 +516,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -537,16 +537,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:07:43.027536377", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:08:27.281315407" + } }, "sarscov2 - [ vcf, tbi ], fasta -stub": { "content": [ @@ -569,7 +569,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -590,16 +590,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:29.018979167", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:14.249715835" + } }, "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub": { "content": [ @@ -622,7 +622,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -643,16 +643,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:59.722987032", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:46.665932019" + } }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index": { "content": [ @@ -673,11 +673,11 @@ ] ] ], + "timestamp": "2024-06-05T07:52:58.381931979", "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" - }, - "timestamp": "2024-06-05T07:52:58.381931979" + } }, "sarscov2 - [ vcf, tbi ], fasta - bcf output - stub": { "content": [ @@ -700,7 +700,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -721,16 +721,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:52.185711106", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:09:38.144449162" + } }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub": { "content": [ @@ -758,7 +758,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -784,16 +784,16 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:09:22.318684414", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:10:10.602984345" + } }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi": { "content": [ @@ -814,11 +814,11 @@ ] ] ], + "timestamp": "2024-06-05T13:53:09.808834237", "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" - }, - "timestamp": "2024-06-05T13:53:09.808834237" + } }, "sarscov2 - [ vcf, tbi ], fasta - bcf output": { "content": [ @@ -841,7 +841,7 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -862,15 +862,15 @@ [ "BCFTOOLS_NORM", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:08:06.045049359", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:08:51.053195842" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginsplit/environment.yml b/modules/nf-core/bcftools/pluginsplit/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/pluginsplit/environment.yml +++ b/modules/nf-core/bcftools/pluginsplit/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf index c83f5911..f8bbcfb2 100644 --- a/modules/nf-core/bcftools/pluginsplit/main.nf +++ b/modules/nf-core/bcftools/pluginsplit/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSPLIT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*"), path(samples), path(groups), path(regions), path(targets) diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap index 624c58ef..cb9fd544 100644 --- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap @@ -23,15 +23,15 @@ [ "BCFTOOLS_PLUGINSPLIT", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-03T13:07:08.893698009", + "timestamp": "2026-03-20T18:16:45.582654411", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi": { @@ -79,15 +79,15 @@ [ "BCFTOOLS_PLUGINSPLIT", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-03T13:14:22.246942262", + "timestamp": "2026-03-20T18:16:24.197265886", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": { @@ -124,15 +124,15 @@ [ "BCFTOOLS_PLUGINSPLIT", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-03T13:15:52.187692008", + "timestamp": "2026-03-20T18:16:59.677975644", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "homo_sapiens - [ vcf, tbi ], samples, [], [], []": { @@ -159,15 +159,15 @@ [ "BCFTOOLS_PLUGINSPLIT", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-03T13:06:40.701929691", + "timestamp": "2026-03-20T18:16:16.876797977", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": { @@ -195,15 +195,15 @@ [ "BCFTOOLS_PLUGINSPLIT", "bcftools", - "1.22" + "1.23.1" ] ] } ], - "timestamp": "2026-03-03T13:14:53.0893172", + "timestamp": "2026-03-20T18:16:52.463665333", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 726360f0..606ce753 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_QUERY { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap index 5168ef3f..2063d2f4 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap @@ -14,16 +14,16 @@ [ "BCFTOOLS_QUERY", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:18:23.300725219", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:16:54.523612853" + } }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ @@ -33,16 +33,16 @@ [ "BCFTOOLS_QUERY", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:18:31.072967763", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:17:00.64798632" + } }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -59,15 +59,15 @@ [ "BCFTOOLS_QUERY", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:18:15.37651846", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:16:47.953130141" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index e0dfad2d..60289a84 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap index 9b9e4dc7..d17a46e7 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -25,7 +25,7 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -51,16 +51,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:21:36.014741519", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:24.286732272" + } }, "vcf": { "content": [ @@ -83,7 +83,7 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -104,16 +104,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:20:42.353160127", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:18:38.783455397" + } }, "sarscov2 - vcf_gz_index": { "content": [ @@ -141,16 +141,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:20:49.824142057", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:18:45.081447395" + } }, "sarscov2 - vcf_gz_index_csi": { "content": [ @@ -178,16 +178,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:20:56.89020695", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:18:51.194304667" + } }, "sarscov2 - vcf_gz_index - stub": { "content": [ @@ -215,7 +215,7 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -241,16 +241,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:21:18.927046854", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:11.413154111" + } }, "sarscov2 - vcf_gz_index_csi - stub": { "content": [ @@ -278,7 +278,7 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -304,16 +304,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:21:27.28878358", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:17.770087535" + } }, "sarscov2 - vcf - stub": { "content": [ @@ -336,7 +336,7 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -357,16 +357,16 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:21:11.928512355", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:04.409593559" + } }, "sarscov2 - vcf_gz_index_tbi": { "content": [ @@ -394,15 +394,15 @@ [ "BCFTOOLS_SORT", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:21:04.275382445", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:18:57.536633502" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index ac77dd5a..3a87361e 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap index 870d364b..1161199b 100644 --- a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - vcf_gz - reference": { "content": [ [ - "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.23.1+htslib-1.23.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --fasta-ref genome.fasta test.vcf.gz", "#", "# Definition of sets:", @@ -10,16 +10,16 @@ "ID\t0\ttest.vcf.gz" ] ], + "timestamp": "2026-03-20T18:22:27.82153528", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T14:58:10.684378" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - vcf_gz - exons": { "content": [ [ - "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.23.1+htslib-1.23.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --exons exons.tsv.gz test.vcf.gz", "#", "# Definition of sets:", @@ -27,11 +27,11 @@ "ID\t0\ttest.vcf.gz" ] ], + "timestamp": "2026-03-20T18:22:18.912655315", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T14:58:05.803224" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "versions": { "content": [ @@ -40,21 +40,21 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:21:53.228681614", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:36.943096649" + } }, "sarscov2 - vcf_gz - targets": { "content": [ [ - "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.23.1+htslib-1.23.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --targets-file test2.targets.tsv.gz test.vcf.gz", "#", "# Definition of sets:", @@ -62,11 +62,11 @@ "ID\t0\ttest.vcf.gz" ] ], + "timestamp": "2026-03-20T18:22:10.341222029", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T14:58:01.121472" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "regions_versions": { "content": [ @@ -75,16 +75,16 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:01.713819348", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:43.504543106" + } }, "targets_versions": { "content": [ @@ -93,16 +93,16 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:10.32795863", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:49.943149098" + } }, "sarscov2 - vcf_gz - stub": { "content": [ @@ -119,7 +119,7 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ], "stats": [ @@ -134,16 +134,16 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:36.639614055", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:09.654761076" + } }, "exon_versions": { "content": [ @@ -152,16 +152,16 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:18.899161374", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:19:56.837252836" + } }, "ref_versions": { "content": [ @@ -170,21 +170,21 @@ [ "BCFTOOLS_STATS", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:27.810279032", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:03.323950267" + } }, "sarscov2 - vcf_gz": { "content": [ [ - "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.23.1+htslib-1.23.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats test.vcf.gz", "#", "# Definition of sets:", @@ -192,16 +192,16 @@ "ID\t0\ttest.vcf.gz" ] ], + "timestamp": "2026-03-20T18:21:53.252674205", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T14:57:51.945138" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } }, "sarscov2 - vcf_gz - regions": { "content": [ [ - "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.23.1+htslib-1.23.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --regions-file test3.vcf.gz test.vcf.gz", "#", "# Definition of sets:", @@ -209,10 +209,10 @@ "ID\t0\ttest.vcf.gz" ] ], + "timestamp": "2026-03-20T18:22:01.726572891", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T14:57:56.50867" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml index ba863b38..01193fda 100644 --- a/modules/nf-core/bcftools/view/environment.yml +++ b/modules/nf-core/bcftools/view/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.22.1 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/bcftools - - bioconda::bcftools=1.22 + - bioconda::bcftools=1.23.1 diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index b3fd7b73..10b9a671 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' - : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data' + : 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}" input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test.snap b/modules/nf-core/bcftools/view/tests/main.nf.test.snap index 92972d19..68926c08 100644 --- a/modules/nf-core/bcftools/view/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/view/tests/main.nf.test.snap @@ -27,7 +27,7 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -55,16 +55,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:46.101707716", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:21:02.710815567" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": { "content": [ @@ -94,16 +94,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:10.374165894", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:36.071823323" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": { "content": [ @@ -133,7 +133,7 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -161,16 +161,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:37.664960008", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:56.054811979" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": { "content": [ @@ -200,7 +200,7 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ], "csi": [ @@ -228,16 +228,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:54.823465363", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:21:09.229049434" + } }, "sarscov2 - [vcf, tbi], vcf, tsv, []": { "content": [ @@ -255,16 +255,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:19.908213867", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:42.68820706" + } }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ @@ -274,16 +274,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:28.40103319", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:49.538986405" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": { "content": [ @@ -313,16 +313,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:53.951814647", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:22.451426124" + } }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -340,16 +340,16 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:22:45.088231326", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:16.040611233" + } }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": { "content": [ @@ -379,15 +379,15 @@ [ "BCFTOOLS_VIEW", "bcftools", - "1.22" + "1.23.1" ] ] } ], + "timestamp": "2026-03-20T18:23:02.014904437", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:20:29.512063514" + } } } \ No newline at end of file diff --git a/modules/nf-core/glimpse2/phase/tests/main.nf.test b/modules/nf-core/glimpse2/phase/tests/main.nf.test index 3f8a1fcf..704bcd8a 100644 --- a/modules/nf-core/glimpse2/phase/tests/main.nf.test +++ b/modules/nf-core/glimpse2/phase/tests/main.nf.test @@ -119,8 +119,9 @@ nextflow_process { file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz", checkIfExists: true), [] ]) - input[2] = [] - input[3] = "crai" + input[2] = [[], []] + input[3] = [[], []] + input[4] = "crai" """ } } diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt new file mode 100644 index 00000000..76190304 --- /dev/null +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt @@ -0,0 +1,1552 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: 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1762979038025 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda +sha256: 66265e943f32ce02396ad214e27cb35f5b0490b3bd4f064446390f9d67fa5d88 +md5: 032d8030e4a24fe1f72c74423a46fb88 +depends: +- libgcc >=14 +license: MIT +license_family: MIT +size: 88088 +timestamp: 1753484092643 +- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda +sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae +md5: 30cd29cb87d819caead4d55184c1d115 +depends: +- python >=3.10 +- python +license: MIT +license_family: MIT +size: 24194 +timestamp: 1764460141901 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda +sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2 +md5: f731af71c723065d91b4c01bb822641b +depends: +- libgcc >=14 +- libstdcxx >=14 +license: Zlib +license_family: Other +size: 121046 +timestamp: 1770167944449 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda +sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75 +md5: c3655f82dcea2aa179b291e7099c1fcc +depends: +- libzlib >=1.3.1,<2.0a0 +license: BSD-3-Clause +license_family: BSD +size: 614429 +timestamp: 1764777145593 diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ef434a9a..57cf43ca 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt linux/arm64: - lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt docker: linux/amd64: - build_id: bd-ee7739d47738383b_1 - name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b - scanId: sc-6ddec592dcadd583_4 + name: community.wave.seqera.io/library/multiqc:1.33--c1f4a7982b743963 + build_id: bd-c1f4a7982b743963_1 + scan_id: sc-b7b7f470b2a16699_1 linux/arm64: - build_id: bd-58d7dee710ab3aa8_1 - name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8 - scanId: sc-a04c42273e34c55c_2 + name: community.wave.seqera.io/library/multiqc:1.33--40bf3b435e89dc22 + build_id: bd-40bf3b435e89dc22_1 + scan_id: sc-0e2108a0e7368d2f_1 singularity: linux/amd64: - build_id: bd-e3576ddf588fa00d_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data - name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d + name: oras://community.wave.seqera.io/library/multiqc:1.33--9b3473b1c4bb0493 + build_id: bd-9b3473b1c4bb0493_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c4/c4e6d9f669e1a99b53c7dc5cdd6b8e7fd6654032c755bb783cc9849e8203f4d1/data linux/arm64: - build_id: bd-2537ca5f8445e3c2_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data - name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2 + name: oras://community.wave.seqera.io/library/multiqc:1.33--e1ef2065eb21b530 + build_id: bd-e1ef2065eb21b530_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2acce766e3efb280fa43acdbe85305ea6496ddadbcaa2d806ac4985dfe4686ce/data diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 0e422eaa..4cbdb95d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -29,13 +29,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -59,13 +72,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -77,7 +103,7 @@ nextflow_process { input[0] = channel.of([ [ id: 'FASTQC' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), - file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), [], [], [] @@ -88,14 +114,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - file(process.out.plots[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -108,8 +146,8 @@ nextflow_process { [ id: 'FASTQC' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), [ - file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true), - file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true) + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) ], [], [], @@ -121,14 +159,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - file(process.out.plots[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c022701f..3bfc524f 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,10 +1,82 @@ { "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", "versions": [ [ "MULTIQC", @@ -14,17 +86,91 @@ ] } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T20:21:35.851707" + } }, "sarscov2 single-end [fastqc]": { "content": [ - "multiqc_report.html", - "multiqc_data", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", "versions": [ [ "MULTIQC", @@ -34,11 +180,11 @@ ] } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:10:36.019680076" + } }, "sarscov2 single-end [fastqc] - stub": { "content": [ @@ -80,18 +226,90 @@ ] } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:14:39.789193051" + } }, "sarscov2 single-end [fastqc] [config]": { "content": [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", "versions": [ [ "MULTIQC", @@ -101,17 +319,91 @@ ] } ], + "timestamp": "2026-03-17T16:15:30.372239611", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:21:29.116129274" + } }, "sarscov2 single-end [fastqc] - custom prefix": { "content": [ - "custom_prefix.html", - "custom_prefix_data", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "custom_prefix.html", "versions": [ [ "MULTIQC", @@ -121,10 +413,10 @@ ] } ], + "timestamp": "2026-03-17T16:15:18.189023981", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:10:43.419877592" + } } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config index c537a6a3..374dfef2 100644 --- a/modules/nf-core/multiqc/tests/nextflow.config +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -1,5 +1,6 @@ process { withName: 'MULTIQC' { ext.prefix = null + ext.args = '-p' } } diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index c257666e..d98baad3 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -81,11 +81,11 @@ ] } ], + "timestamp": "2026-02-06T12:45:34.563809348", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T12:45:34.563809348" + } }, "QUILT no optional files": { "content": [ @@ -138,11 +138,11 @@ ] } ], + "timestamp": "2026-02-06T12:45:44.999545443", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T12:45:44.999545443" + } }, "QUILT with bamlist and renaming": { "content": [ @@ -195,11 +195,11 @@ ] } ], + "timestamp": "2026-02-06T12:45:55.703650448", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T12:45:55.703650448" + } }, "homo_sapiens - bam, hap, legend, posfile, phasefile, map - fasta": { "content": [ @@ -209,7 +209,7 @@ "id": "NA12878", "chr": "chr22" }, - "NA12878.vcf.gz.tbi:md5,da74a7127dff516779a73e560010ec12" + "NA12878.vcf.gz.tbi:md5,f4e800b09116b8ccac8e62c0f835eeed" ] ], [ @@ -253,7 +253,7 @@ "chr": "chr22" }, [ - "QUILT_prepared_reference.chr22.16570000.16610000.RData:md5,d4ba79eb3450d7892c5e9ee77d61e361" + "QUILT_prepared_reference.chr22.16570000.16610000.RData:md5,2c025b29d2cfde0fd4b2de062bd1db19" ] ] ], @@ -266,7 +266,7 @@ [ "NA12878" ], - "f5c315626c7b8dc416e9804234db46bf" + "df1391e233c9a8b237e0f77e188ee2b7" ] ], { @@ -286,10 +286,10 @@ ] } ], + "timestamp": "2026-03-23T01:54:01.765873438", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T12:43:37.723599456" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf index 31fcbb65..b0d90964 100644 --- a/modules/nf-core/samtools/coverage/main.nf +++ b/modules/nf-core/samtools/coverage/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COVERAGE { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap index 85380d1f..359a9599 100644 --- a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap @@ -14,7 +14,7 @@ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -23,7 +23,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:01:01.345508" + "timestamp": "2026-03-19T08:56:33.66881" }, "test_samtools_coverage_bam": { "content": [ @@ -40,7 +40,7 @@ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -49,7 +49,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:00:38.855929" + "timestamp": "2026-03-19T08:56:13.846408" }, "test_samtools_coverage_cram": { "content": [ @@ -66,7 +66,7 @@ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23" + "1.23.1" ] ], "coverage": [ @@ -81,7 +81,7 @@ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -90,6 +90,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:00:45.230154" + "timestamp": "2026-03-19T08:56:19.040435" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 01051d72..b6e770aa 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_DEPTH { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta1), path(bam), path(index) diff --git a/modules/nf-core/samtools/depth/tests/main.nf.test.snap b/modules/nf-core/samtools/depth/tests/main.nf.test.snap index 581f61b0..1be81bed 100644 --- a/modules/nf-core/samtools/depth/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/depth/tests/main.nf.test.snap @@ -14,7 +14,7 @@ [ "SAMTOOLS_DEPTH", "samtools", - "1.23" + "1.23.1" ] ], "tsv": [ @@ -29,7 +29,7 @@ [ "SAMTOOLS_DEPTH", "samtools", - "1.23" + "1.23.1" ] ] } @@ -38,7 +38,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:04:07.545677" + "timestamp": "2026-03-19T08:57:04.203477" }, "test-samtools-depth": { "content": [ @@ -55,7 +55,7 @@ [ "SAMTOOLS_DEPTH", "samtools", - "1.23" + "1.23.1" ] ], "tsv": [ @@ -70,7 +70,7 @@ [ "SAMTOOLS_DEPTH", "samtools", - "1.23" + "1.23.1" ] ] } @@ -79,7 +79,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:03:06.521821" + "timestamp": "2026-03-19T08:56:55.125056" }, "test-samtools-depth -- stub": { "content": [ @@ -96,7 +96,7 @@ [ "SAMTOOLS_DEPTH", "samtools", - "1.23" + "1.23.1" ] ], "tsv": [ @@ -111,7 +111,7 @@ [ "SAMTOOLS_DEPTH", "samtools", - "1.23" + "1.23.1" ] ] } @@ -120,6 +120,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:05:55.270281" + "timestamp": "2026-03-19T08:57:14.281531" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 7741419f..4ff3fd70 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta), path(fasta), path(fai) diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index d1770085..e879d962 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -23,7 +23,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -32,7 +32,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:10:28.314852" + "timestamp": "2026-03-19T08:57:29.747964" }, "test_samtools_faidx_get_sizes_bgzip - stub": { "content": [ @@ -68,7 +68,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -77,7 +77,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:11:23.529047" + "timestamp": "2026-03-19T08:58:10.04235" }, "test_samtools_faidx_get_sizes": { "content": [ @@ -108,7 +108,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -117,7 +117,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:11:03.69393" + "timestamp": "2026-03-19T08:57:55.552612" }, "test_samtools_faidx_bgzip": { "content": [ @@ -148,7 +148,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -157,7 +157,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:10:36.32865" + "timestamp": "2026-03-19T08:57:34.346045" }, "test_samtools_faidx_fasta": { "content": [ @@ -183,7 +183,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -192,7 +192,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:10:42.889457" + "timestamp": "2026-03-19T08:57:39.136814" }, "test_samtools_faidx_get_sizes - stub": { "content": [ @@ -223,7 +223,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -232,7 +232,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:11:17.768704" + "timestamp": "2026-03-19T08:58:05.200994" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -258,7 +258,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -267,7 +267,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:10:49.769431" + "timestamp": "2026-03-19T08:57:44.105654" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -293,7 +293,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -302,7 +302,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:10:56.943681" + "timestamp": "2026-03-19T08:57:50.839162" }, "test_samtools_faidx_get_sizes_bgzip": { "content": [ @@ -338,7 +338,7 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23" + "1.23.1" ] ] } @@ -347,6 +347,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:11:11.899364" + "timestamp": "2026-03-19T08:58:00.460031" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 46c46802..ad3c1533 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 6e677e6e..337dec77 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -15,17 +15,16 @@ [ "SAMTOOLS_INDEX", "samtools", - "1.23" + "1.23.1" ] ] } ], - "timestamp": "2026-03-12T15:13:55.847467933", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:33:18.224422" + "timestamp": "2026-03-19T09:00:39.171613" }, "crai - stub": { "content": [ @@ -43,17 +42,16 @@ [ "SAMTOOLS_INDEX", "samtools", - "1.23" + "1.23.1" ] ] } ], - "timestamp": "2026-03-12T15:13:49.297141274", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:33:12.325309" + "timestamp": "2026-03-19T09:00:32.838795" }, "bai - stub": { "content": [ @@ -71,17 +69,16 @@ [ "SAMTOOLS_INDEX", "samtools", - "1.23" + "1.23.1" ] ] } ], - "timestamp": "2026-03-12T15:13:41.627654374", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:32:39.811759" + "timestamp": "2026-03-19T09:00:25.255379" }, "csi": { "content": [ @@ -91,17 +88,16 @@ [ "SAMTOOLS_INDEX", "samtools", - "1.23" + "1.23.1" ] ] } ], - "timestamp": "2026-03-12T15:13:34.664832363", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:32:33.879034" + "timestamp": "2026-03-19T09:00:18.414839" }, "crai": { "content": [ @@ -119,17 +115,16 @@ [ "SAMTOOLS_INDEX", "samtools", - "1.23" + "1.23.1" ] ] } ], - "timestamp": "2026-03-12T15:13:27.854803902", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:32:28.01812" + "timestamp": "2026-03-19T09:00:13.571297" }, "bai": { "content": [ @@ -147,16 +142,15 @@ [ "SAMTOOLS_INDEX", "samtools", - "1.23" + "1.23.1" ] ] } ], - "timestamp": "2026-03-12T15:13:18.782751979", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:31:52.203411" + "timestamp": "2026-03-19T09:00:06.767362" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index c93d7862..eb122551 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta), path(input_files, stageAs: "?/*"), path(index_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index 3f8df81e..77ed449d 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -20,7 +20,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ], "bam": [ @@ -41,7 +41,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -50,7 +50,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-13T18:10:40.861374" + "timestamp": "2026-03-19T09:01:31.816184" }, "crams_fastq": { "content": [ @@ -64,7 +64,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -73,7 +73,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-13T18:11:53.506628" + "timestamp": "2026-03-19T09:01:05.719443" }, "bams - stub": { "content": [ @@ -96,7 +96,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ], "bam": [ @@ -117,7 +117,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -126,7 +126,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-13T18:10:33.945617" + "timestamp": "2026-03-19T09:01:24.795562" }, "bams": { "content": [ @@ -140,7 +140,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -149,7 +149,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-13T18:11:44.959682" + "timestamp": "2026-03-19T09:00:59.536803" }, "crams_fastq_gz": { "content": [ @@ -163,7 +163,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -172,7 +172,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-13T18:12:02.35866" + "timestamp": "2026-03-19T09:01:11.614088" }, "bam": { "content": [ @@ -188,7 +188,7 @@ [ "SAMTOOLS_MERGE", "samtools", - "1.23" + "1.23.1" ] ] } @@ -197,6 +197,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-13T18:12:09.17774" + "timestamp": "2026-03-19T09:01:17.736424" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/reheader/main.nf b/modules/nf-core/samtools/reheader/main.nf index bd10d254..928a15e9 100644 --- a/modules/nf-core/samtools/reheader/main.nf +++ b/modules/nf-core/samtools/reheader/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_REHEADER { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/reheader/tests/main.nf.test.snap b/modules/nf-core/samtools/reheader/tests/main.nf.test.snap index 1cdfe008..03925c19 100644 --- a/modules/nf-core/samtools/reheader/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/reheader/tests/main.nf.test.snap @@ -7,14 +7,14 @@ { "id": "test" }, - "test_reheaded.bam:md5,0c5436974ec6b504219da1f26a8788c3" + "test_reheaded.bam:md5,2d9486de8f40a6d9de3ccf8dbf8d36dc" ] ], "1": [ [ "SAMTOOLS_REHEADER", "samtools", - "1.23" + "1.23.1" ] ], "bam": [ @@ -22,14 +22,14 @@ { "id": "test" }, - "test_reheaded.bam:md5,0c5436974ec6b504219da1f26a8788c3" + "test_reheaded.bam:md5,2d9486de8f40a6d9de3ccf8dbf8d36dc" ] ], "versions_samtools": [ [ "SAMTOOLS_REHEADER", "samtools", - "1.23" + "1.23.1" ] ] } @@ -38,7 +38,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:38:06.71878" + "timestamp": "2026-03-19T09:02:52.263978" }, "homo_sapiens - stub": { "content": [ @@ -55,7 +55,7 @@ [ "SAMTOOLS_REHEADER", "samtools", - "1.23" + "1.23.1" ] ], "bam": [ @@ -70,16 +70,16 @@ [ "SAMTOOLS_REHEADER", "samtools", - "1.23" + "1.23.1" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T17:09:21.267386117" + "timestamp": "2026-03-19T09:03:03.921419" }, "homo_sapiens - rgdel": { "content": [ @@ -89,14 +89,14 @@ { "id": "test" }, - "test_reheaded.bam:md5,44f53924708f994c5c3cc70c5ed2d902" + "test_reheaded.bam:md5,2efc4859a23bd18e9684a41d48ce1096" ] ], "1": [ [ "SAMTOOLS_REHEADER", "samtools", - "1.23" + "1.23.1" ] ], "bam": [ @@ -104,14 +104,14 @@ { "id": "test" }, - "test_reheaded.bam:md5,44f53924708f994c5c3cc70c5ed2d902" + "test_reheaded.bam:md5,2efc4859a23bd18e9684a41d48ce1096" ] ], "versions_samtools": [ [ "SAMTOOLS_REHEADER", "samtools", - "1.23" + "1.23.1" ] ] } @@ -120,6 +120,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T14:38:13.401816" + "timestamp": "2026-03-19T09:02:57.299464" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 0b1446fd..946bb362 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23 + - bioconda::htslib=1.23.1 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index fd5027f1..724561bf 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,13 +4,14 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" input: tuple val(meta), path(input), path(index) tuple val(meta2), path(fasta), path(fai) - path qname + tuple val(meta3), path(qname) + tuple val(meta4), path(bed) val index_format output: @@ -43,6 +44,7 @@ process SAMTOOLS_VIEW { output_file = index_format ? "${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_format} --write-index" : "${prefix}.${file_type}" // Can't choose index type of unselected file readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}" : "" + def bedfile = bed ? "-L ${bed}" : "" if ("${input}" == "${prefix}.${file_type}") { error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") @@ -62,6 +64,7 @@ process SAMTOOLS_VIEW { --threads ${task.cpus - 1} \\ ${reference} \\ ${readnames} \\ + ${bedfile} \\ ${args} \\ -o ${output_file} \\ ${input} \\ diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 33e60c45..51e31834 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -49,11 +49,27 @@ input: pattern: "*.{fai}" ontologies: - edam: http://edamontology.org/format_3326 # Index - - qname: - type: file - description: Optional file with read names to output only select alignments - pattern: "*.{txt,list}" - ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" + ontologies: [] + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Optional BED file for filtering alignments by genomic region (-L) + pattern: "*.{bed}" + ontologies: + - edam: http://edamontology.org/format_3003 # BED - index_format: type: string description: Index format, used together with ext.args = '--write-index' diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 8d8f292f..12faf1f1 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -23,8 +23,9 @@ nextflow_process { [] ] input[1] = [[],[],[]] - input[2] = [] - input[3] = [] + input[2] = [[], []] + input[3] = [[], []] + input[4] = [] """ } } @@ -50,8 +51,9 @@ nextflow_process { [] ] input[1] = [[],[],[]] - input[2] = [] - input[3] = 'csi' + input[2] = [[], []] + input[3] = [[], []] + input[4] = 'csi' """ } } @@ -77,8 +79,9 @@ nextflow_process { [] ] input[1] = [[],[],[]] - input[2] = [] - input[3] = 'bai' + input[2] = [[], []] + input[3] = [[], []] + input[4] = 'bai' """ } } @@ -106,7 +109,9 @@ nextflow_process { input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') - input[3] = 'bai' + .map { file -> [[:], file] } + input[3] = [[], []] + input[4] = 'bai' """ } } @@ -134,7 +139,9 @@ nextflow_process { input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') - input[3] = 'crai' + .map { file -> [[:], file] } + input[3] = [[], []] + input[4] = 'crai' """ } } @@ -164,8 +171,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = [] - input[3] = [] + input[2] = [[], []] + input[3] = [[], []] + input[4] = [] """ } } @@ -195,8 +203,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = [] - input[3] = [] + input[2] = [[], []] + input[3] = [[], []] + input[4] = [] """ } } @@ -226,8 +235,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = [] - input[3] = [] + input[2] = [[], []] + input[3] = [[], []] + input[4] = [] """ } } @@ -259,7 +269,9 @@ nextflow_process { ] input[2] = Channel.of("testN:2817", "testN:2814") .collectFile(name: "readnames.list", newLine: true) - input[3] = [] + .map { file -> [[:], file] } + input[3] = [[], []] + input[4] = [] """ } } @@ -272,6 +284,37 @@ nextflow_process { } } + test("bam_with_bed") { + when { + params { + samtools_args = "--output-fmt bam" + } + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [[],[],[]] + input[2] = [[], []] + input[3] = [ + [:], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()} + ) + } + } + test("bam_stub") { options "-stub" @@ -288,8 +331,9 @@ nextflow_process { [] ] input[1] = [[],[],[]] - input[2] = [] - input[3] = [] + input[2] = [[], []] + input[3] = [[], []] + input[4] = [] """ } } @@ -318,8 +362,9 @@ nextflow_process { [] ] input[1] = [[],[],[]] - input[2] = [] - input[3] = 'csi' + input[2] = [[], []] + input[3] = [[], []] + input[4] = 'csi' """ } } @@ -348,8 +393,9 @@ nextflow_process { [] ] input[1] = [[],[],[]] - input[2] = [] - input[3] = 'bai' + input[2] = [[], []] + input[3] = [[], []] + input[4] = 'bai' """ } } @@ -380,7 +426,9 @@ nextflow_process { input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') - input[3] = 'bai' + .map { file -> [[:], file] } + input[3] = [[], []] + input[4] = 'bai' """ } } @@ -411,7 +459,9 @@ nextflow_process { input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') - input[3] = 'crai' + .map { file -> [[:], file] } + input[3] = [[], []] + input[4] = 'crai' """ } } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index deb306a8..697c918d 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -40,16 +40,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:44.475595", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:14.82588493" + "nextflow": "25.10.4" + } }, "bam_csi_index - stub": { "content": [ @@ -92,7 +92,7 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ], "bai": [ @@ -133,16 +133,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:07:04.977559", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:31.409368544" + "nextflow": "25.10.4" + } }, "bam_csi_index": { "content": [ @@ -185,16 +185,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:07.203393", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:48:46.36824035" + "nextflow": "25.10.4" + } }, "cram_to_bam_index_qname": { "content": [ @@ -221,7 +221,7 @@ { "id": "test" }, - "test.bam.csi:md5,9e42ca315563f048b85ebd14ffa2a807" + "test.bam.csi:md5,15d725bced7ececd45b4312b2af99a6b" ] ], "sam": [ @@ -247,16 +247,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:52.242422", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-12T14:51:01.408213" + } }, "bam_bai_index_unselected": { "content": [ @@ -309,16 +309,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:18.267421", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:48:57.713608154" + "nextflow": "25.10.4" + } }, "cram_crai_index_unselected - stub": { "content": [ @@ -371,7 +371,7 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ], "bai": [ @@ -422,16 +422,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:07:27.864649", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:48.092654899" + "nextflow": "25.10.4" + } }, "bam": { "content": [ @@ -469,16 +469,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:01.906355", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:48:27.608944526" + "nextflow": "25.10.4" + } }, "bam_bai_index": { "content": [ @@ -521,16 +521,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:12.483533", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:48:52.047178732" + "nextflow": "25.10.4" + } }, "cram_to_bam": { "content": [ @@ -568,16 +568,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:37.592685", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:50:41.727031999" + "nextflow": "25.10.4" + } }, "bam_bai_index - stub": { "content": [ @@ -620,7 +620,7 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ], "bai": [ @@ -661,16 +661,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:07:12.214174", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:36.783381688" + "nextflow": "25.10.4" + } }, "cram": { "content": [ @@ -708,16 +708,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:29.867409", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:09.393102901" + "nextflow": "25.10.4" + } }, "bam_bai_index_uselected - stub": { "content": [ @@ -770,7 +770,7 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ], "bai": [ @@ -821,16 +821,63 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:07:21.14353", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:42.344755528" + "nextflow": "25.10.4" + } + }, + "bam_with_bed": { + "content": [ + { + "bai": [ + + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.23.1" + ] + ] + } + ], + "timestamp": "2026-03-25T12:13:59.0656", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "cram_crai_index_unselected": { "content": [ @@ -854,7 +901,7 @@ { "id": "test" }, - "test.cram:md5,24cce9e8ff83a3c3010c7319b3627d07" + "test.cram:md5,924e27301c54060128cc259f5f83e74f" ] ], "csi": [ @@ -883,16 +930,16 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:23.90307", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-12T14:50:35.160451" + } }, "bam_stub": { "content": [ @@ -935,15 +982,15 @@ [ "SAMTOOLS_VIEW", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-03-19T09:06:58.641723", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T16:49:26.152824543" + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/nextflow.config b/modules/nf-core/samtools/view/tests/nextflow.config index cd059134..7d11b502 100644 --- a/modules/nf-core/samtools/view/tests/nextflow.config +++ b/modules/nf-core/samtools/view/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: SAMTOOLS_VIEW { - ext.args = params.samtools_args + ext.args = { params.samtools_args } } } diff --git a/modules/nf-core/shapeit5/ligate/main.nf b/modules/nf-core/shapeit5/ligate/main.nf index dc0a477b..99bf7a6c 100644 --- a/modules/nf-core/shapeit5/ligate/main.nf +++ b/modules/nf-core/shapeit5/ligate/main.nf @@ -9,6 +9,7 @@ process SHAPEIT5_LIGATE { input: tuple val(meta), path(input_list), path(input_list_index) + val suffix_ output: tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: merged_variants @@ -20,7 +21,8 @@ process SHAPEIT5_LIGATE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "vcf.gz" + def suffix = suffix_ ?: "vcf.gz" + assert suffix in ["vcf", "vcf.gz", "bcf", "bcf.gz"] // Create file list using Groovy (most portable) def file_list = input_list @@ -40,8 +42,8 @@ process SHAPEIT5_LIGATE { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "vcf.gz" - + def suffix = suffix_ ?: "vcf.gz" + assert suffix in ["vcf", "vcf.gz", "bcf", "bcf.gz"] def create_cmd = suffix.endsWith(".gz") ? "echo '' | gzip >" : "touch" """ ${create_cmd} ${prefix}.${suffix} diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml index d95c0b66..cc67720a 100644 --- a/modules/nf-core/shapeit5/ligate/meta.yml +++ b/modules/nf-core/shapeit5/ligate/meta.yml @@ -34,6 +34,10 @@ input: description: VCF/BCF files index. pattern: "*.csi" ontologies: [] + - suffix_: + type: string + description: Output format + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" output: merged_variants: - - meta: diff --git a/modules/nf-core/shapeit5/ligate/tests/main.nf.test b/modules/nf-core/shapeit5/ligate/tests/main.nf.test index b3b826a1..7cbbadc9 100644 --- a/modules/nf-core/shapeit5/ligate/tests/main.nf.test +++ b/modules/nf-core/shapeit5/ligate/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { input[0] = BCFTOOLS_VIEW.out.vcf.join(BCFTOOLS_VIEW.out.csi) .map{ meta, vcf, index -> [meta.subMap("id"), vcf, index]} .groupTuple() + input[1] = '' """ } } @@ -73,6 +74,7 @@ nextflow_process { [file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz", checkIfExists: true)], [file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi", checkIfExists: true)] ] + input[1] = '' """ } } diff --git a/subworkflows/local/bam_extract_region_samtools/main.nf b/subworkflows/local/bam_extract_region_samtools/main.nf index dbaf4d64..85f4cda0 100644 --- a/subworkflows/local/bam_extract_region_samtools/main.nf +++ b/subworkflows/local/bam_extract_region_samtools/main.nf @@ -22,7 +22,8 @@ workflow BAM_EXTRACT_REGION_SAMTOOLS { SAMTOOLS_VIEW( ch_input_region, [[], [], []], - [], + [[], []], + [[], []], "csi" ) diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf index b7cc8759..2427d275 100644 --- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf @@ -10,10 +10,8 @@ include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { samplesheetToList } from 'plugin/nf-schema' -include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { paramsSummaryMap } from 'plugin/nf-schema' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' @@ -472,7 +470,7 @@ workflow PIPELINE_COMPLETION { completionSummary(monochrome_logs) if (hook_url) { - imNotification(summary_params, hook_url) + log.warn("`--hook_url` is set, but the updated nf-core utility subworkflow no longer provides instant messaging notifications. The value will be ignored.") } } diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/meta.yml b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/meta.yml new file mode 100644 index 00000000..eda69f12 --- /dev/null +++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/meta.yml @@ -0,0 +1,49 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PHASEIMPUTE_PIPELINE" +description: | + Local utility subworkflow for nf-core/phaseimpute that prepares input channels, + validates pipeline inputs, and handles completion reporting hooks. +keywords: + - utils + - nf-core + - phaseimpute + - schema +components: + - utils_nfschema_plugin + - utils_nfcore_pipeline + - utils_nextflow_pipeline + - samtools/faidx +input: + - version: + type: boolean + description: Print workflow version and exit + - validate_params: + type: boolean + description: Validate pipeline parameters + - nextflow_cli_args: + type: list + description: Positional Nextflow CLI arguments + - outdir: + type: string + description: Output directory for pipeline artefacts +output: + - input: + description: Prepared pipeline input channel + - input_truth: + description: Prepared truth input channel + - fasta: + description: Prepared reference channel + - panel: + description: Prepared panel channel + - depth: + description: Prepared depth channel + - regions: + description: Prepared regions channel + - gmap: + description: Prepared genetic map channel + - posfile: + description: Prepared posfile channel + - chunks: + description: Prepared chunk channel + - chunk_model: + description: Selected chunking model diff --git a/subworkflows/local/vcf_sites_extract_bcftools/meta.yml b/subworkflows/local/vcf_sites_extract_bcftools/meta.yml index fbe558c4..6784d7b0 100644 --- a/subworkflows/local/vcf_sites_extract_bcftools/meta.yml +++ b/subworkflows/local/vcf_sites_extract_bcftools/meta.yml @@ -9,6 +9,8 @@ keywords: components: - bcftools/view - bcftools/convert + - gawk + - tabix/bgzip input: - ch_vcf: type: file diff --git a/subworkflows/nf-core/bam_impute_quilt/tests/main.nf.test.snap b/subworkflows/nf-core/bam_impute_quilt/tests/main.nf.test.snap index 28d938b1..f08da13f 100644 --- a/subworkflows/nf-core/bam_impute_quilt/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_impute_quilt/tests/main.nf.test.snap @@ -22,11 +22,11 @@ ] } ], + "timestamp": "2026-02-06T14:04:32.890807138", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T14:04:32.890807138" + } }, "Impute with quilt one individual, no renaming, posfile, no chunks, no map, no fasta": { "content": [ @@ -42,11 +42,11 @@ ] ] ], + "timestamp": "2026-02-06T14:03:25.847677815", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T14:03:25.847677815" + } }, "Impute with quilt two individual bam, renaming, posfile, chunks, map, no fasta": { "content": [ @@ -69,14 +69,14 @@ "MySample1", "MySample2" ], - "3a47675c78aacc7c0a385284160f4c07" + "be6669035788ceefce326b05b0ae3475" ] ] ], + "timestamp": "2026-03-23T01:55:26.163837539", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-06T14:04:14.879818839" + "nf-test": "0.9.4", + "nextflow": "25.10.2" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_impute_stitch/tests/main.nf.test.snap b/subworkflows/nf-core/bam_impute_stitch/tests/main.nf.test.snap index ec3b695c..e7b1a6d7 100644 --- a/subworkflows/nf-core/bam_impute_stitch/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_impute_stitch/tests/main.nf.test.snap @@ -73,14 +73,14 @@ "MySample1", "MySample2" ], - "88ee8bbae9712d3f791f3df2c3eb0ab3" + "ac38db1b020d33a9ca1fa5e75858b51" ] ] ], - "timestamp": "2026-03-03T09:28:32.060465639", + "timestamp": "2026-03-23T01:54:35.936985907", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf b/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf index 94beb8f6..31d9f527 100644 --- a/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf +++ b/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf @@ -35,7 +35,8 @@ workflow BAM_SUBSAMPLEDEPTH_SAMTOOLS { SAMTOOLS_VIEW( ch_input_subsample, ch_fasta, - [], + [[], []], + [[], []], [] ) diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap index 2fb2b66e..6f700e05 100644 --- a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap @@ -9,8 +9,8 @@ "subsample_fraction": 0.06201800538763442, "depth": 2 }, - "NA12878.bam:md5,8dee1728966da1f834c3578175b1a615", - "NA12878.bam.csi:md5,0b4abd161cdcc2b51571c9cc651df354", + "NA12878.bam:md5,0793ec4585bd0fb64be4643c0e9f6d1f", + "NA12878.bam.csi:md5,e117d88fd3409d42f3cf97b3b29dba22", 1164 ], [ @@ -20,8 +20,8 @@ "subsample_fraction": 0.12403601077526884, "depth": 4 }, - "NA12878.bam:md5,b0e902359d79996fde0c31ef1529b401", - "NA12878.bam.csi:md5,3f8f9a17463b6c2391c632681d3f253a", + "NA12878.bam:md5,2ce0a90fb85a2a6c0dac4f1555abee04", + "NA12878.bam.csi:md5,d1f24a25181d75c19f3ba169898b5678", 2402 ], [ @@ -31,8 +31,8 @@ "subsample_fraction": 0.062137851766009305, "depth": 2 }, - "NA19401.bam:md5,1bc911be27df51534201c3a377f0e965", - "NA19401.bam.csi:md5,36c29896003f2de5306ff427a969058c", + "NA19401.bam:md5,d678ed2b80b76d5c0ee305be1c11c7dc", + "NA19401.bam.csi:md5,3c33431336c405d971f9b69724310b87", 1196 ], [ @@ -42,8 +42,8 @@ "subsample_fraction": 0.12427570353201861, "depth": 4 }, - "NA19401.bam:md5,4944ab61569bc2f1f9da41f6dbbc0948", - "NA19401.bam.csi:md5,b44701d7d4de827cc1b83aaeb397deaf", + "NA19401.bam:md5,1d19189dae93fd5b76a2644ab45ef14c", + "NA19401.bam.csi:md5,14a9e8d58a46360917263c22c07dea41", 2321 ] ] @@ -52,6 +52,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-12T11:09:08.47406" + "timestamp": "2026-03-19T10:24:20.82405" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/tests/main.nf.test.snap index 50538978..c749af80 100644 --- a/subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/tests/main.nf.test.snap @@ -15,13 +15,13 @@ ] ], [ - "NA12878_22.bcftools_stats.txt:md5,e35386eaea9c0047d0c9ce56ae966d10" + "NA12878_22.bcftools_stats.txt:md5,99e061326bb518f555db886788420467" ] ], - "timestamp": "2026-02-27T18:26:40.379067986", + "timestamp": "2026-03-23T01:55:41.061652061", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.2" } }, "Two individuals and two chromosomes, sort and annotate": { @@ -40,16 +40,16 @@ ] ], [ - "NA12878_21.bcftools_stats.txt:md5,29f310e5ed86cc2d3f6f77eb5da2a7e0", - "NA12878_22.bcftools_stats.txt:md5,e35386eaea9c0047d0c9ce56ae966d10", - "NA19401_21.bcftools_stats.txt:md5,16730f1e8df6e0446ed2779d87c98168", - "NA19401_22.bcftools_stats.txt:md5,e9b457859517dcfaf886335cbbe442b3" + "NA12878_21.bcftools_stats.txt:md5,090d000383fe17fedac8e9834a5cf2eb", + "NA12878_22.bcftools_stats.txt:md5,99e061326bb518f555db886788420467", + "NA19401_21.bcftools_stats.txt:md5,c8bd18b1f2b1426a2e7a4204489a12a9", + "NA19401_22.bcftools_stats.txt:md5,21caaa358f27a5722dd508e7aac1954b" ] ], - "timestamp": "2026-03-02T13:24:14.07373231", + "timestamp": "2026-03-23T01:55:27.347884175", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "One individual and two chromosomes": { @@ -68,14 +68,14 @@ ] ], [ - "NA12878_21.bcftools_stats.txt:md5,29f310e5ed86cc2d3f6f77eb5da2a7e0", - "NA12878_22.bcftools_stats.txt:md5,e35386eaea9c0047d0c9ce56ae966d10" + "NA12878_21.bcftools_stats.txt:md5,090d000383fe17fedac8e9834a5cf2eb", + "NA12878_22.bcftools_stats.txt:md5,99e061326bb518f555db886788420467" ] ], - "timestamp": "2026-02-27T18:26:57.619510735", + "timestamp": "2026-03-23T01:55:55.943228912", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.2" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 2f30e9a4..bf568a08 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) { log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) { - misc_fields['repository'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['commitid'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['revision'] = workflow.revision - } - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection() - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")) - def postRC = post.getResponseCode() - if (!postRC.equals(200)) { - log.warn(post.getErrorStream().getText()) - } -} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test similarity index 100% rename from subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test rename to subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap similarity index 100% rename from subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap rename to subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index ee4738c8..1df8b76f 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - params.help instanceof String ? params.help : "", + (params.help instanceof String && params.help != "true") ? params.help : "", ) exit 0 } @@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN { emit: dummy_emit = true } - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 8d8c7371..f6537cc3 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.5.1" + id "nf-schema@2.6.1" } validation { diff --git a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf index 6e6afbb7..70914db0 100644 --- a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf +++ b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf @@ -85,7 +85,7 @@ workflow VCF_PHASE_SHAPEIT5 { } .groupTuple() - SHAPEIT5_LIGATE(ch_ligate_input) + SHAPEIT5_LIGATE(ch_ligate_input,'') BCFTOOLS_INDEX_LIGATE(SHAPEIT5_LIGATE.out.merged_variants) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e38073ff..c42f2b60 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -8,10 +8,10 @@ "samtools": "1.23" }, "BCFTOOLS_ANNOTATE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -20,19 +20,19 @@ "bcftools": "1.23.1" }, "BCFTOOLS_MERGE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_MPILEUP": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "CUSTOM_GENETICMAPCONVERT": { "r-base": "4.5.3", @@ -52,7 +52,7 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -193,15 +193,15 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878_chr21.bcftools_stats.txt:md5,b3c191449997ee25d185dd72ef19a388", - "NA12878_chr22.bcftools_stats.txt:md5,2acad3c5394652caca75e30c3dbb5c8a", - "NA19401_chr21.bcftools_stats.txt:md5,7c61050c739598419b0fd0f14bed5d52", - "NA19401_chr22.bcftools_stats.txt:md5,9d3e897e1c797884020044909919b9cd", - "NA20359_chr21.bcftools_stats.txt:md5,0e6e8f12e2f983a56812286e638cd0af", - "NA20359_chr22.bcftools_stats.txt:md5,63edc6b74ab77cb3d89a59997f892603", - "NA12878.glimpse1.bcftools_stats.txt:md5,d712e30d7f2450ca22c905421f006494", - "NA19401.glimpse1.bcftools_stats.txt:md5,86efb7502150bfcdd60a77c35e78de64", - "NA20359.glimpse1.bcftools_stats.txt:md5,62b33ff85651520eab02ac21dd4995ec", + "NA12878_chr21.bcftools_stats.txt:md5,f6504c9a043268651cc70aade534e5e8", + "NA12878_chr22.bcftools_stats.txt:md5,41f17b319c7dbf47be9015971710f5d2", + "NA19401_chr21.bcftools_stats.txt:md5,3ef1da38844a20a9c8709b397b4c4adf", + "NA19401_chr22.bcftools_stats.txt:md5,52998d0e36b72d0041f1553106401482", + "NA20359_chr21.bcftools_stats.txt:md5,0a18a5824ed6b3958bd3b3d3f0cc44c0", + "NA20359_chr22.bcftools_stats.txt:md5,a0c62ca49ef39b6cb03442a3f9ce224c", + "NA12878.glimpse1.bcftools_stats.txt:md5,ef6b20f1b0bec03c7ac61375a5474119", + "NA19401.glimpse1.bcftools_stats.txt:md5,2920962fbdd91e31850baa9be89dd912", + "NA20359.glimpse1.bcftools_stats.txt:md5,726b11871cf8e4223e11b9ef820f5279", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", diff --git a/workflows/phaseimpute/tests/test_all.nf.test.snap b/workflows/phaseimpute/tests/test_all.nf.test.snap index f9006d8e..4004054a 100644 --- a/workflows/phaseimpute/tests/test_all.nf.test.snap +++ b/workflows/phaseimpute/tests/test_all.nf.test.snap @@ -11,13 +11,13 @@ "samtools": "1.23" }, "BCFTOOLS_ANNOTATE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONVERT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" @@ -29,34 +29,34 @@ "bcftools": "1.23.1" }, "BCFTOOLS_MERGE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_MPILEUP": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_NORM": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_TRUTH": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_PANEL": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TRUTH": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_VIEW": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { "tabix": "1.21" @@ -117,25 +117,25 @@ "r-quilt": "1.0.5" }, "SAMTOOLS_COVERAGE_DWN": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_COVERAGE_INP": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_DEPTH": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_INDEX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_MERGE": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_VIEW": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SHAPEIT5_LIGATE": { "shapeit5": "5.1.1" @@ -558,24 +558,24 @@ "all_samples.batch0.id.txt:md5,a4c01a39309f9522d5b01108e3b75c64", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,276f71c6daa405e34b4b88783aeef913", - "NA12878_chr21.bcftools_stats.txt:md5,69d11621ec148b39d4bba59f6871537b", - "NA12878_chr22.bcftools_stats.txt:md5,2733db49dc260c001a554e2ff947f7e9", - "NA19401_chr21.bcftools_stats.txt:md5,c2824ec5d1994fe5d4295fcb73f4d9a2", - "NA19401_chr22.bcftools_stats.txt:md5,1cd2010dba151a5712acec88e8c63846", - "NA20359_chr21.bcftools_stats.txt:md5,50657f5d7f9d8595e22e9e77c3cbbb42", - "NA20359_chr22.bcftools_stats.txt:md5,bed65c27dc7754ab6b40bbfedee1aed1", - "NA12878.glimpse1.bcftools_stats.txt:md5,d712e30d7f2450ca22c905421f006494", - "NA12878.glimpse2.bcftools_stats.txt:md5,4551f4274b0c2e04d6c8f41454dc9b88", - "NA12878.quilt.bcftools_stats.txt:md5,06be906390f87548cff77877dff5c981", - "NA12878.stitch.bcftools_stats.txt:md5,6991969d019398e8704ea4cb269a315b", - "NA19401.glimpse1.bcftools_stats.txt:md5,86efb7502150bfcdd60a77c35e78de64", - "NA19401.glimpse2.bcftools_stats.txt:md5,cca5d4895da3203386fa9ee061044d12", - "NA19401.quilt.bcftools_stats.txt:md5,eaf59f02e81aeaafdc1953e92687d5d0", - "NA19401.stitch.bcftools_stats.txt:md5,2370cce588665aa328b941a0bd1a847e", - "NA20359.glimpse1.bcftools_stats.txt:md5,62b33ff85651520eab02ac21dd4995ec", - "NA20359.glimpse2.bcftools_stats.txt:md5,fa7efcf9b006db08bd66e61f54d04f4a", - "NA20359.quilt.bcftools_stats.txt:md5,24972d94b67f8d0bcfe88fa052c1f279", - "NA20359.stitch.bcftools_stats.txt:md5,752a126486b629de8a34f826ade67086", + "NA12878_chr21.bcftools_stats.txt:md5,847cef4148300c99a1d0f38dd5d1ff1d", + "NA12878_chr22.bcftools_stats.txt:md5,de2d69ed3c6b84939f42389caf3ff89c", + "NA19401_chr21.bcftools_stats.txt:md5,25f10bf15228c746d2874ab12dfcc0a2", + "NA19401_chr22.bcftools_stats.txt:md5,5be0bec78d2932918b2f77fcc9ed659d", + "NA20359_chr21.bcftools_stats.txt:md5,ab48d1c2dc3f128a21d4b78ca8211738", + "NA20359_chr22.bcftools_stats.txt:md5,4755c511cf3a5dd090b560f526f25749", + "NA12878.glimpse1.bcftools_stats.txt:md5,ef6b20f1b0bec03c7ac61375a5474119", + "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", + "NA12878.quilt.bcftools_stats.txt:md5,ca99e46fc6a4b76ee47396b07664f861", + "NA12878.stitch.bcftools_stats.txt:md5,24d54d3ffba3fed39f7824abbf9a7d81", + "NA19401.glimpse1.bcftools_stats.txt:md5,2920962fbdd91e31850baa9be89dd912", + "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", + "NA19401.quilt.bcftools_stats.txt:md5,17f18a5af11c51c902511588b96e0482", + "NA19401.stitch.bcftools_stats.txt:md5,360b697eac096a9b0ae2cc1059659418", + "NA20359.glimpse1.bcftools_stats.txt:md5,726b11871cf8e4223e11b9ef820f5279", + "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", + "NA20359.quilt.bcftools_stats.txt:md5,0905fc06908d4482a5f06e11a04a8ffb", + "NA20359.stitch.bcftools_stats.txt:md5,6d62a564c7fead78240007ac90bc8e3b", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,30837458e3113f0dd225e3255f3f60ec", @@ -619,7 +619,7 @@ "1000GP.chr22.posfile.txt.gz:md5,f5997df5995dcdbc4ab31e1084b83541", "1000GP.chr21.posfile.txt:md5,33d064c5132000799f3df9ea31967e12", "1000GP.chr22.posfile.txt:md5,f5997df5995dcdbc4ab31e1084b83541", - "1000GP.panel.bcftools_stats.txt:md5,ca5eb47541961f3b757c83b77a307a5f", + "1000GP.panel.bcftools_stats.txt:md5,d01ec3426d5dda525b21da1c62a6c6fd", "NA12878_Call.depth.mean.tsv:md5,713a1f4811ad68444bffa85d1fcdbe0d", "NA12878_Call.depth.tsv:md5,ad4748275377d3241aff21cddd97d1e7", "NA19401_Call.depth.mean.tsv:md5,aab44099c9906b1619cad70830bedf7e", @@ -627,17 +627,17 @@ "NA20359_Call.depth.mean.tsv:md5,caec5b47dd4f370753b500eb3cf101c4", "NA20359_Call.depth.tsv:md5,1cc9ee6a593493a0368976cff8d16d49", "AllSamples.txt:md5,7532ffd859efbbf854efa6110b3c4e4f", - "NA12878.truth.bcftools_stats.txt:md5,ceee2009cd4a74d74baf170d32f66952", + "NA12878.truth.bcftools_stats.txt:md5,f7e940f7d822c519eff426aa316e9c51", "NA12878_P1000GP_Tglimpse1_SNP.txt:md5,2528024cd7013dcbb14aa2af665a1064", "NA12878_P1000GP_Tglimpse2_SNP.txt:md5,3c85cfdfe3bcde49ac4e8dd63ffe8fe0", "NA12878_P1000GP_Tquilt_SNP.txt:md5,bd09185888d528a2b32536eb6d804182", "NA12878_P1000GP_Tstitch_SNP.txt:md5,f34c239b4f10654fa8db1a8998abc3fe", - "NA19401.truth.bcftools_stats.txt:md5,43291b0c73e060d00cde702b7d0887fb", + "NA19401.truth.bcftools_stats.txt:md5,74a6c16b24adff3aae779946866e1a1f", "NA19401_P1000GP_Tglimpse1_SNP.txt:md5,675b2558732855d74075e273a1403260", "NA19401_P1000GP_Tglimpse2_SNP.txt:md5,f9716583bf003939801d8a6f89547088", "NA19401_P1000GP_Tquilt_SNP.txt:md5,b2457a395c68491e87868b1190c37453", "NA19401_P1000GP_Tstitch_SNP.txt:md5,a471c4da4f5290f97a9d397fe7caba30", - "NA20359.truth.bcftools_stats.txt:md5,df053793f79724f1967ace49f13eafc1", + "NA20359.truth.bcftools_stats.txt:md5,a17a4fe97555879bc74336fb71f18cbe", "NA20359_P1000GP_Tglimpse1_SNP.txt:md5,f23379c2009de5aad1258cca9e8a5b1e", "NA20359_P1000GP_Tglimpse2_SNP.txt:md5,84ad7cc8aedc6ceeee899730de8c5315", "NA20359_P1000GP_Tquilt_SNP.txt:md5,e3dee1e6b8b36c2b3feb7d0bf4d9515c", @@ -986,25 +986,25 @@ "nextflow": "26.04.0" } }, - "Check test_all - with map": { + "Check test_all": { "content": [ { - "workflow size": 247, + "workflow size": 245, "versions": { "ADDCOLUMNS": { "gawk": "5.3.1" }, "BAMCHREXTRACT": { - "samtools": "1.23" + "samtools": 1.23 }, "BCFTOOLS_ANNOTATE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONVERT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" @@ -1016,42 +1016,37 @@ "bcftools": "1.23.1" }, "BCFTOOLS_MERGE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_MPILEUP": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_NORM": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_TRUTH": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_PANEL": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TRUTH": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_VIEW": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { - "tabix": "1.21" - }, - "CUSTOM_GENETICMAPCONVERT": { - "r-base": "4.5.3", - "r-data.table": "1.17.8", - "r-janitor": "2.2.1" + "tabix": 1.21 }, "FILTER_CHR_DWN": { "gawk": "5.3.1" @@ -1099,7 +1094,7 @@ "glimpse": "1.1.1" }, "GUNZIP": { - "gunzip": "1.13" + "gunzip": 1.13 }, "LISTTOFILE": { "gawk": "5.3.1" @@ -1109,25 +1104,1011 @@ "r-quilt": "1.0.5" }, "SAMTOOLS_COVERAGE_DWN": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_COVERAGE_INP": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_DEPTH": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_INDEX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_MERGE": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_VIEW": { - "samtools": "1.23" + "samtools": "1.23.1" + }, + "SHAPEIT5_LIGATE": { + "shapeit5": "5.1.1" + }, + "SHAPEIT5_PHASECOMMON": { + "shapeit5": "5.1.1" + }, + "STITCH": { + "r-base": "4.4.2", + "r-quilt": "1.7.3", + "rsync": "3.4.1" + }, + "TABIX_BGZIP": { + "tabix": 1.21 + }, + "TABIX_TABIX": { + "tabix": 1.21 + }, + "VCFCHREXTRACT": { + "bcftools": 1.22 + }, + "VCFLIB_VCFFIXUP": { + "vcflib": "1.0.14" + }, + "Workflow": { + "nf-core/phaseimpute": "v1.2.0dev" + } + }, + "stable name": [ + "imputation", + "imputation/batch", + "imputation/batch/all_samples.batch0.id.txt", + "imputation/batch/all_samples.batch0.idonly.txt", + "imputation/batch/all_samples.batch0.noid.txt", + "imputation/csv", + "imputation/csv/impute.csv", + "imputation/glimpse1", + "imputation/glimpse1/concat", + "imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz", + "imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/impute", + "imputation/glimpse1/impute/all_samples.batch0.chr21.ligate.glimpse1.vcf.gz", + "imputation/glimpse1/impute/all_samples.batch0.chr21.ligate.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/impute/all_samples.batch0.chr21_16570070-16590513.glimpse1.bcf.csi", + "imputation/glimpse1/impute/all_samples.batch0.chr21_16590521-16609998.glimpse1.bcf.csi", + "imputation/glimpse1/impute/all_samples.batch0.chr22.ligate.glimpse1.vcf.gz", + "imputation/glimpse1/impute/all_samples.batch0.chr22.ligate.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/impute/all_samples.batch0.chr22_16570065-16592216.glimpse1.bcf.csi", + "imputation/glimpse1/impute/all_samples.batch0.chr22_16592229-16609999.glimpse1.bcf.csi", + "imputation/glimpse1/samples", + "imputation/glimpse1/samples/NA12878.glimpse1.vcf.gz", + "imputation/glimpse1/samples/NA12878.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/samples/NA19401.glimpse1.vcf.gz", + "imputation/glimpse1/samples/NA19401.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/samples/NA20359.glimpse1.vcf.gz", + "imputation/glimpse1/samples/NA20359.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/variant_calling", + 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"NA19401,NA19401.depth_1x.bam,NA19401.depth_1x.bam.csi", + "NA20359,NA20359.depth_1x.bam,NA20359.depth_1x.bam.csi" + ] + } + ] + }, + { + "all_samples.glimpse1": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", + "samples": [ + "NA12878", + "NA19401", + "NA20359" + ] + }, + "all_samples.glimpse2": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", + "samples": [ + "NA12878", + "NA19401", + "NA20359" + ] + }, + "all_samples.quilt": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", + "samples": [ + "NA12878", + "NA19401", + "NA20359" + ] + }, + "all_samples.stitch": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", + "samples": [ + "NA12878", + "NA19401", + "NA20359" + ] + } + } + ], + "timestamp": "2026-04-12T20:03:45.613944785", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "Check test_all - with map": { + "content": [ + { + "workflow size": 247, + "versions": { + "ADDCOLUMNS": { + "gawk": "5.3.1" + }, + "BAMCHREXTRACT": { + "samtools": "1.23" + }, + "BCFTOOLS_ANNOTATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_CONCAT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_CONVERT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_LIGATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_PHASE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_MERGE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_MPILEUP": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_NORM": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_PLUGINSPLIT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_QUERY_IMPUTED": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_QUERY_TRUTH": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_STATS_PANEL": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_STATS_TOOLS": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_STATS_TRUTH": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_VIEW": { + "bcftools": "1.23.1" + }, + "BGZIP_POSFILE_IMPUTE": { + "tabix": "1.21" + }, + "CUSTOM_GENETICMAPCONVERT": { + "r-base": "4.5.3", + "r-data.table": "1.17.8", + "r-janitor": "2.2.1" + }, + "FILTER_CHR_DWN": { + "gawk": "5.3.1" + }, + "FILTER_CHR_INP": { + "gawk": "5.3.1" + }, + "GAWK": { + "gawk": "5.3.1" + }, + "GAWK_ERROR_SPL": { + "gawk": "5.3.1" + }, + "GAWK_IMPUTED": { + "gawk": "5.3.1" + }, + "GAWK_POSFILE_IMPUTE": { + "gawk": "5.3.1" + }, + "GAWK_RSQUARE_SPL": { + "gawk": "5.3.1" + }, + "GAWK_TRUTH": { + "gawk": "5.3.1" + }, + "GLIMPSE2_CHUNK": { + "glimpse2": "2.0.0" + }, + "GLIMPSE2_CONCORDANCE": { + "glimpse2": "2.0.0" + }, + "GLIMPSE2_LIGATE": { + "glimpse2": "2.0.0" + }, + "GLIMPSE2_PHASE": { + "glimpse2": "2.0.0" + }, + "GLIMPSE_CHUNK": { + "glimpse": "1.1.1" + }, + "GLIMPSE_LIGATE": { + "glimpse": "1.1.1" + }, + "GLIMPSE_PHASE": { + "glimpse": "1.1.1" + }, + "GUNZIP": { + "gunzip": "1.13" + }, + "LISTTOFILE": { + "gawk": "5.3.1" + }, + "QUILT_QUILT": { + "r-base": "4.3.1", + "r-quilt": "1.0.5" + }, + "SAMTOOLS_COVERAGE_DWN": { + "samtools": "1.23.1" + }, + "SAMTOOLS_COVERAGE_INP": { + "samtools": "1.23.1" + }, + "SAMTOOLS_DEPTH": { + "samtools": "1.23.1" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.23.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.23.1" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.23.1" + }, + "SAMTOOLS_VIEW": { + "samtools": "1.23.1" }, "SHAPEIT5_LIGATE": { "shapeit5": "5.1.1" @@ -1559,24 +2540,24 @@ "all_samples.batch0.id.txt:md5,a4c01a39309f9522d5b01108e3b75c64", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,276f71c6daa405e34b4b88783aeef913", - "NA12878_chr21.bcftools_stats.txt:md5,69d11621ec148b39d4bba59f6871537b", - "NA12878_chr22.bcftools_stats.txt:md5,2733db49dc260c001a554e2ff947f7e9", - "NA19401_chr21.bcftools_stats.txt:md5,c2824ec5d1994fe5d4295fcb73f4d9a2", - "NA19401_chr22.bcftools_stats.txt:md5,1cd2010dba151a5712acec88e8c63846", - "NA20359_chr21.bcftools_stats.txt:md5,50657f5d7f9d8595e22e9e77c3cbbb42", - "NA20359_chr22.bcftools_stats.txt:md5,bed65c27dc7754ab6b40bbfedee1aed1", - "NA12878.glimpse1.bcftools_stats.txt:md5,d712e30d7f2450ca22c905421f006494", - "NA12878.glimpse2.bcftools_stats.txt:md5,4551f4274b0c2e04d6c8f41454dc9b88", - "NA12878.quilt.bcftools_stats.txt:md5,06be906390f87548cff77877dff5c981", - "NA12878.stitch.bcftools_stats.txt:md5,6991969d019398e8704ea4cb269a315b", - "NA19401.glimpse1.bcftools_stats.txt:md5,86efb7502150bfcdd60a77c35e78de64", - "NA19401.glimpse2.bcftools_stats.txt:md5,cca5d4895da3203386fa9ee061044d12", - "NA19401.quilt.bcftools_stats.txt:md5,eaf59f02e81aeaafdc1953e92687d5d0", - "NA19401.stitch.bcftools_stats.txt:md5,2370cce588665aa328b941a0bd1a847e", - "NA20359.glimpse1.bcftools_stats.txt:md5,62b33ff85651520eab02ac21dd4995ec", - "NA20359.glimpse2.bcftools_stats.txt:md5,fa7efcf9b006db08bd66e61f54d04f4a", - "NA20359.quilt.bcftools_stats.txt:md5,24972d94b67f8d0bcfe88fa052c1f279", - "NA20359.stitch.bcftools_stats.txt:md5,752a126486b629de8a34f826ade67086", + "NA12878_chr21.bcftools_stats.txt:md5,847cef4148300c99a1d0f38dd5d1ff1d", + "NA12878_chr22.bcftools_stats.txt:md5,de2d69ed3c6b84939f42389caf3ff89c", + "NA19401_chr21.bcftools_stats.txt:md5,25f10bf15228c746d2874ab12dfcc0a2", + "NA19401_chr22.bcftools_stats.txt:md5,5be0bec78d2932918b2f77fcc9ed659d", + "NA20359_chr21.bcftools_stats.txt:md5,ab48d1c2dc3f128a21d4b78ca8211738", + "NA20359_chr22.bcftools_stats.txt:md5,4755c511cf3a5dd090b560f526f25749", + "NA12878.glimpse1.bcftools_stats.txt:md5,ef6b20f1b0bec03c7ac61375a5474119", + "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", + "NA12878.quilt.bcftools_stats.txt:md5,ca99e46fc6a4b76ee47396b07664f861", + "NA12878.stitch.bcftools_stats.txt:md5,24d54d3ffba3fed39f7824abbf9a7d81", + "NA19401.glimpse1.bcftools_stats.txt:md5,2920962fbdd91e31850baa9be89dd912", + "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", + "NA19401.quilt.bcftools_stats.txt:md5,17f18a5af11c51c902511588b96e0482", + "NA19401.stitch.bcftools_stats.txt:md5,360b697eac096a9b0ae2cc1059659418", + "NA20359.glimpse1.bcftools_stats.txt:md5,726b11871cf8e4223e11b9ef820f5279", + "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", + "NA20359.quilt.bcftools_stats.txt:md5,0905fc06908d4482a5f06e11a04a8ffb", + "NA20359.stitch.bcftools_stats.txt:md5,6d62a564c7fead78240007ac90bc8e3b", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", @@ -1628,7 +2609,7 @@ "1000GP.chr22.posfile.txt.gz:md5,f5997df5995dcdbc4ab31e1084b83541", "1000GP.chr21.posfile.txt:md5,33d064c5132000799f3df9ea31967e12", "1000GP.chr22.posfile.txt:md5,f5997df5995dcdbc4ab31e1084b83541", - "1000GP.panel.bcftools_stats.txt:md5,ca5eb47541961f3b757c83b77a307a5f", + "1000GP.panel.bcftools_stats.txt:md5,d01ec3426d5dda525b21da1c62a6c6fd", "NA12878_Call.depth.mean.tsv:md5,713a1f4811ad68444bffa85d1fcdbe0d", "NA12878_Call.depth.tsv:md5,ad4748275377d3241aff21cddd97d1e7", "NA19401_Call.depth.mean.tsv:md5,aab44099c9906b1619cad70830bedf7e", @@ -1636,17 +2617,17 @@ "NA20359_Call.depth.mean.tsv:md5,caec5b47dd4f370753b500eb3cf101c4", "NA20359_Call.depth.tsv:md5,1cc9ee6a593493a0368976cff8d16d49", "AllSamples.txt:md5,5c70da51580ea7bdfaca4c13723f595c", - "NA12878.truth.bcftools_stats.txt:md5,ceee2009cd4a74d74baf170d32f66952", + "NA12878.truth.bcftools_stats.txt:md5,f7e940f7d822c519eff426aa316e9c51", "NA12878_P1000GP_Tglimpse1_SNP.txt:md5,fccb27b1c226ff15033f6d18f5171fa6", "NA12878_P1000GP_Tglimpse2_SNP.txt:md5,5a34211c0e442c39b98b8cf55acca7ee", "NA12878_P1000GP_Tquilt_SNP.txt:md5,19312d9e1b72fcaa82d27b636faa671b", "NA12878_P1000GP_Tstitch_SNP.txt:md5,22734b924f523387f0ae01aedcef75ed", - "NA19401.truth.bcftools_stats.txt:md5,43291b0c73e060d00cde702b7d0887fb", + "NA19401.truth.bcftools_stats.txt:md5,74a6c16b24adff3aae779946866e1a1f", "NA19401_P1000GP_Tglimpse1_SNP.txt:md5,7239a14e0f42795d25ec4a26b60d0420", "NA19401_P1000GP_Tglimpse2_SNP.txt:md5,8abadd9af91a53ec4b4867102fe79ae7", "NA19401_P1000GP_Tquilt_SNP.txt:md5,ba7c787fe59cc4a36cf72c3543884f76", "NA19401_P1000GP_Tstitch_SNP.txt:md5,95a37a51c90106a71d25bbb8b498960e", - "NA20359.truth.bcftools_stats.txt:md5,df053793f79724f1967ace49f13eafc1", + "NA20359.truth.bcftools_stats.txt:md5,a17a4fe97555879bc74336fb71f18cbe", "NA20359_P1000GP_Tglimpse1_SNP.txt:md5,22618ec6a3a24c3a8abde6907c56d451", "NA20359_P1000GP_Tglimpse2_SNP.txt:md5,c9dacfcc715610d9ec7faad32e7063c0", "NA20359_P1000GP_Tquilt_SNP.txt:md5,afd9373b6b8fb3ddf6a726f0889f8952", diff --git a/workflows/phaseimpute/tests/test_batch.nf.test.snap b/workflows/phaseimpute/tests/test_batch.nf.test.snap index 27d33fae..a8fb8961 100644 --- a/workflows/phaseimpute/tests/test_batch.nf.test.snap +++ b/workflows/phaseimpute/tests/test_batch.nf.test.snap @@ -11,7 +11,7 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" @@ -23,22 +23,22 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_TRUTH": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_PANEL": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TRUTH": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { "tabix": "1.21" @@ -81,7 +81,7 @@ "r-quilt": "1.0.5" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -300,12 +300,12 @@ "all_samples.batch1.id.txt:md5,41d3f29a40566b10760e53b4112b9cb9", "all_samples.batch1.idonly.txt:md5,5732a4ed24904236f034a6e13be24cff", "all_samples.batch1.noid.txt:md5,cc74a26d0a0449bdb003ce20644996b7", - "NA12878.glimpse2.bcftools_stats.txt:md5,4551f4274b0c2e04d6c8f41454dc9b88", - "NA12878.quilt.bcftools_stats.txt:md5,06be906390f87548cff77877dff5c981", - "NA19401.glimpse2.bcftools_stats.txt:md5,cca5d4895da3203386fa9ee061044d12", - "NA19401.quilt.bcftools_stats.txt:md5,eaf59f02e81aeaafdc1953e92687d5d0", - "NA20359.glimpse2.bcftools_stats.txt:md5,fa7efcf9b006db08bd66e61f54d04f4a", - "NA20359.quilt.bcftools_stats.txt:md5,24972d94b67f8d0bcfe88fa052c1f279", + "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", + "NA12878.quilt.bcftools_stats.txt:md5,ca99e46fc6a4b76ee47396b07664f861", + "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", + "NA19401.quilt.bcftools_stats.txt:md5,17f18a5af11c51c902511588b96e0482", + "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", + "NA20359.quilt.bcftools_stats.txt:md5,0905fc06908d4482a5f06e11a04a8ffb", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,325c6b7429ecf340b8bda9c8d2a6d79f", @@ -327,15 +327,15 @@ "multiqc_general_stats.txt:md5,55ffda22b30bf13174fc8c81047d6ed7", "multiqc_glimpse_err_grp.txt:md5,7303ceb7e80ab2b188f2dd355b6a1498", "multiqc_glimpse_err_spl.txt:md5,b59190a0f0295ec4da4a6527980c874d", - "1000GP.panel.bcftools_stats.txt:md5,ca5eb47541961f3b757c83b77a307a5f", + "1000GP.panel.bcftools_stats.txt:md5,d01ec3426d5dda525b21da1c62a6c6fd", "AllSamples.txt:md5,5bbc52fa94514bc7fca3cc345a7db6c0", - "NA12878.truth.bcftools_stats.txt:md5,edf521ce34766a8f9063fd88297bb869", + "NA12878.truth.bcftools_stats.txt:md5,4e8153cc6be1b8ebe1a460be78ef252f", "NA12878_P1000GP_Tglimpse2_SNP.txt:md5,8b1e30077b2d79f678ba18a54614cd95", "NA12878_P1000GP_Tquilt_SNP.txt:md5,e0001f03ebd16bff3ce24fe82ae54656", - "NA19401.truth.bcftools_stats.txt:md5,57e1ae30a08fd25cfca3bce9dcf68b95", + "NA19401.truth.bcftools_stats.txt:md5,acde3c70c921f7fa2f98f8d5463b43b7", "NA19401_P1000GP_Tglimpse2_SNP.txt:md5,bb657ce7e1378e6e30e2e01e7af347f2", "NA19401_P1000GP_Tquilt_SNP.txt:md5,07f89127662623c61ea126b9d8c9abb6", - "NA20359.truth.bcftools_stats.txt:md5,d38bf9d569b4ebaaf0ec263791a29b39", + "NA20359.truth.bcftools_stats.txt:md5,cef8ca0e4df2d9768077eaf4c88df6e6", "NA20359_P1000GP_Tglimpse2_SNP.txt:md5,da7ce6c0f54c442fda1ff612cf5c5d09", "NA20359_P1000GP_Tquilt_SNP.txt:md5,7d0ef6423bf4ea9346765db912779dcc" ], diff --git a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap b/workflows/phaseimpute/tests/test_beagle5.nf.test.snap index 3f3b986a..b9b05331 100644 --- a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap +++ b/workflows/phaseimpute/tests/test_beagle5.nf.test.snap @@ -1,11 +1,198 @@ { + "Check test_beagle5 - without chunks": { + "content": [ + { + "workflow size": 49, + "versions": { + "BCFTOOLS_CONCAT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_LIGATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_PHASE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_PLUGINSPLIT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_QUERY_IMPUTED": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_STATS_TOOLS": { + "bcftools": "1.23.1" + }, + "BEAGLE5_BEAGLE": { + "beagle": 5.5 + }, + "GAWK_IMPUTED": { + "gawk": "5.3.1" + }, + "GLIMPSE2_LIGATE": { + "glimpse2": "2.0.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.23.1" + }, + "TABIX_TABIX": { + "tabix": 1.21 + }, + "VCFCHREXTRACT": { + "bcftools": 1.22 + }, + "Workflow": { + "nf-core/phaseimpute": "v1.2.0dev" + } + }, + "stable name": [ + "imputation", + "imputation/beagle5", + "imputation/beagle5/concat", + "imputation/beagle5/concat/NA12878.beagle5.vcf.gz", + "imputation/beagle5/concat/NA12878.beagle5.vcf.gz.tbi", + "imputation/beagle5/concat/NA19401.beagle5.vcf.gz", + "imputation/beagle5/concat/NA19401.beagle5.vcf.gz.tbi", + "imputation/beagle5/concat/NA20359.beagle5.vcf.gz", + "imputation/beagle5/concat/NA20359.beagle5.vcf.gz.tbi", + "imputation/beagle5/samples", + "imputation/beagle5/samples/NA12878.beagle5.vcf.gz", + "imputation/beagle5/samples/NA12878.beagle5.vcf.gz.tbi", + "imputation/beagle5/samples/NA19401.beagle5.vcf.gz", + "imputation/beagle5/samples/NA19401.beagle5.vcf.gz.tbi", + "imputation/beagle5/samples/NA20359.beagle5.vcf.gz", + "imputation/beagle5/samples/NA20359.beagle5.vcf.gz.tbi", + "imputation/csv", + "imputation/csv/impute.csv", + "imputation/stats", + "imputation/stats/NA12878.beagle5.bcftools_stats.txt", + "imputation/stats/NA19401.beagle5.bcftools_stats.txt", + "imputation/stats/NA20359.beagle5.bcftools_stats.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_bcftools_stats.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + 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"9929895add4b9d27277980f889a0fdf3" + ] + ], + "CSV files": [ + { + "fileName": "impute.csv", + "rows": [ + "sample,tools,file,index", + "NA12878,beagle5,NA12878.beagle5.vcf.gz,NA12878.beagle5.vcf.gz.tbi", + "NA19401,beagle5,NA19401.beagle5.vcf.gz,NA19401.beagle5.vcf.gz.tbi", + "NA20359,beagle5,NA20359.beagle5.vcf.gz,NA20359.beagle5.vcf.gz.tbi" + ] + } + ] + }, + { + "NA12878.beagle5": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=1, variantCount=1739, phased=true]", + "samples": [ + "NA12878" + ] + } + } + ], + "timestamp": "2026-04-12T20:12:04.725212918", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "Check test_beagle5 - with chunks - with map": { + "content": [ + { + "workflow size": 51, + "versions": { + "BCFTOOLS_CONCAT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_LIGATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_PHASE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_PLUGINSPLIT": { + "bcftools": "1.23.1" + }, + 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"1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", diff --git a/workflows/phaseimpute/tests/test_dog.nf.test.snap b/workflows/phaseimpute/tests/test_dog.nf.test.snap index 9758ee98..72f24807 100644 --- a/workflows/phaseimpute/tests/test_dog.nf.test.snap +++ b/workflows/phaseimpute/tests/test_dog.nf.test.snap @@ -8,13 +8,13 @@ "samtools": "1.23" }, "BCFTOOLS_ANNOTATE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONVERT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" @@ -26,19 +26,19 @@ "bcftools": "1.23.1" }, "BCFTOOLS_MPILEUP": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_VIEW": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { "tabix": "1.21" @@ -78,7 +78,7 @@ "r-quilt": "1.0.5" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SHAPEIT5_LIGATE": { "shapeit5": "5.1.1" @@ -269,11 +269,11 @@ "all_samples.batch0.id.txt:md5,2181a5165013a23885b1b8c986765963", "all_samples.batch0.idonly.txt:md5,b8903a12c45a3a7d10a69ee27f502c87", "all_samples.batch0.noid.txt:md5,3efb890bd71c27e79d736153c6870953", - "dog_1735_chr21.bcftools_stats.txt:md5,23aeb26a018cd10f2a6ea305d17d8e5e", - "dog_1735_chr22.bcftools_stats.txt:md5,180907c857f787ea824c9999567487a9", - "dog_1735.glimpse1.bcftools_stats.txt:md5,d8e81c6461489ab484959a2db84f249c", - "dog_1735.glimpse2.bcftools_stats.txt:md5,3dcefcccb3a8e51608356c02cb9190b0", - "dog_1735.quilt.bcftools_stats.txt:md5,4aa056976d4b87fbc7f458d4ce5c39b3", + "dog_1735_chr21.bcftools_stats.txt:md5,a599d34b0d39174acea89e0dc085edf0", + "dog_1735_chr22.bcftools_stats.txt:md5,75a471d34226b99959c22b8ced67e6ad", + "dog_1735.glimpse1.bcftools_stats.txt:md5,470737fb4c91a2d3538be073466dadbc", + "dog_1735.glimpse2.bcftools_stats.txt:md5,877409263beac77f7bdd92209a27c7f3", + "dog_1735.quilt.bcftools_stats.txt:md5,4c7c23540dd225babb82840e9aba2e5d", "canFam3.s.fa.gz.fai:md5,631682a5849e271d84f3bf628418a6d7", "canFam3.s.fa.gz.gzi:md5,b0a77162749742f3372b26e0b4f81565", "bcftools-stats-subtypes.txt:md5,9397a3e17ce0d48f612401c6b5af1c07", diff --git a/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap b/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap index 29e89969..dde14b51 100644 --- a/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap +++ b/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap @@ -8,10 +8,896 @@ "samtools": "1.23" }, "BCFTOOLS_ANNOTATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_CONCAT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_LIGATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_PHASE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_MERGE": { + "bcftools": "1.23.1" 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"BAMCHREXTRACT": { + "samtools": 1.23 + }, + "BCFTOOLS_ANNOTATE": { + "bcftools": "1.23.1" + }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -20,19 +906,19 @@ "bcftools": "1.23.1" }, "BCFTOOLS_MERGE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_MPILEUP": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "GAWK_IMPUTED": { "gawk": "5.3.1" @@ -47,13 +933,13 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { - "tabix": "1.21" + "tabix": 1.21 }, "VCFCHREXTRACT": { - "bcftools": "1.22" + "bcftools": 1.22 }, "Workflow": { "nf-core/phaseimpute": "v1.2.0dev" @@ -116,10 +1002,6 @@ "imputation/stats/NA12878.glimpse1.bcftools_stats.txt", 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"NA19401.glimpse1.bcftools_stats.txt:md5,2920962fbdd91e31850baa9be89dd912", + "NA20359.glimpse1.bcftools_stats.txt:md5,726b11871cf8e4223e11b9ef820f5279", "bcftools-stats-subtypes.txt:md5,bda6ac9e13fd82da1c4725287937332d", "bcftools_stats_indel-lengths.txt:md5,ee1c3af6586e9f8de2f20f759a7741eb", "bcftools_stats_variant_depths.txt:md5,4c05005171167a0ca6824cbff8f7ddb4", @@ -306,10 +1186,10 @@ "samtools": "1.23" }, "BCFTOOLS_ANNOTATE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -318,19 +1198,19 @@ "bcftools": "1.23.1" }, "BCFTOOLS_MERGE": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_MPILEUP": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" 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"2026-04-12T20:15:24.90442267", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Check test_glimpse2 - with chunks - with map": { "content": [ { @@ -8,7 +388,7 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -17,13 +397,13 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "CUSTOM_GENETICMAPCONVERT": { "r-base": "4.5.3", @@ -43,7 +423,7 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -144,9 +524,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.glimpse2.bcftools_stats.txt:md5,4551f4274b0c2e04d6c8f41454dc9b88", - "NA19401.glimpse2.bcftools_stats.txt:md5,cca5d4895da3203386fa9ee061044d12", - "NA20359.glimpse2.bcftools_stats.txt:md5,fa7efcf9b006db08bd66e61f54d04f4a", + "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", + "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", + "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", @@ -226,7 +606,7 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -235,13 +615,13 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "GAWK_IMPUTED": { "gawk": "5.3.1" @@ -256,7 +636,7 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -348,9 +728,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.glimpse2.bcftools_stats.txt:md5,4551f4274b0c2e04d6c8f41454dc9b88", - "NA19401.glimpse2.bcftools_stats.txt:md5,cca5d4895da3203386fa9ee061044d12", - "NA20359.glimpse2.bcftools_stats.txt:md5,fa7efcf9b006db08bd66e61f54d04f4a", + "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", + "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", + "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,9c74a2688bd333bd9c9919476514258e", diff --git a/workflows/phaseimpute/tests/test_minimac4.nf.test.snap b/workflows/phaseimpute/tests/test_minimac4.nf.test.snap index c46915b3..1186a963 100644 --- a/workflows/phaseimpute/tests/test_minimac4.nf.test.snap +++ b/workflows/phaseimpute/tests/test_minimac4.nf.test.snap @@ -5,7 +5,7 @@ "workflow size": 65, "versions": { "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -14,13 +14,13 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "CUSTOM_GENETICMAPCONVERT": { "r-base": "4.5.3", @@ -40,7 +40,7 @@ "minimac4": "4.1.6" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -138,9 +138,9 @@ "pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml" ], "stable path": [ - "NA12878.minimac4.bcftools_stats.txt:md5,36118c4128a03608a9aa39fab426fcfe", - "NA19401.minimac4.bcftools_stats.txt:md5,dd7ded8ca642151ca96a281b7410bffb", - "NA20359.minimac4.bcftools_stats.txt:md5,aadca3e840500a903413e9c14e6fedd0", + "NA12878.minimac4.bcftools_stats.txt:md5,5af867d3d54f3cdbc9dfcb5e7e651449", + "NA19401.minimac4.bcftools_stats.txt:md5,5b3b724bced2bed3b1c5f646cfaa9f92", + "NA20359.minimac4.bcftools_stats.txt:md5,7b0580f0a386be26e33e724b18647d03", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", @@ -223,7 +223,7 @@ "workflow size": 63, "versions": { "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -232,13 +232,13 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "GAWK_IMPUTED": { "gawk": "5.3.1" @@ -253,7 +253,7 @@ "minimac4": "4.1.6" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -342,9 +342,9 @@ "pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml" ], "stable path": [ - "NA12878.minimac4.bcftools_stats.txt:md5,36118c4128a03608a9aa39fab426fcfe", - "NA19401.minimac4.bcftools_stats.txt:md5,dd7ded8ca642151ca96a281b7410bffb", - "NA20359.minimac4.bcftools_stats.txt:md5,aadca3e840500a903413e9c14e6fedd0", + "NA12878.minimac4.bcftools_stats.txt:md5,5af867d3d54f3cdbc9dfcb5e7e651449", + "NA19401.minimac4.bcftools_stats.txt:md5,5b3b724bced2bed3b1c5f646cfaa9f92", + "NA20359.minimac4.bcftools_stats.txt:md5,7b0580f0a386be26e33e724b18647d03", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,a6ea6fbba2fab0d9899174bee8f9c68f", diff --git a/workflows/phaseimpute/tests/test_panelprep.nf.test.snap b/workflows/phaseimpute/tests/test_panelprep.nf.test.snap index 015d1de7..3f79c482 100644 --- a/workflows/phaseimpute/tests/test_panelprep.nf.test.snap +++ b/workflows/phaseimpute/tests/test_panelprep.nf.test.snap @@ -5,7 +5,7 @@ "workflow size": 34, "versions": { "BCFTOOLS_CONVERT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" @@ -17,10 +17,10 @@ "bcftools": "1.23.1" }, "BCFTOOLS_NORM": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_VIEW": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "CUSTOM_GENETICMAPCONVERT": { "r-base": "4.5.3", @@ -31,7 +31,7 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SHAPEIT5_LIGATE": { "shapeit5": "5.1.1" @@ -225,7 +225,7 @@ "workflow size": 36, "versions": { "BCFTOOLS_CONVERT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" @@ -237,10 +237,10 @@ "bcftools": "1.23.1" }, "BCFTOOLS_NORM": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_VIEW": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "GAWK": { "gawk": "5.3.1" @@ -252,7 +252,7 @@ "glimpse": "1.1.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SHAPEIT5_LIGATE": { "shapeit5": "5.1.1" diff --git a/workflows/phaseimpute/tests/test_quilt.nf.test.snap b/workflows/phaseimpute/tests/test_quilt.nf.test.snap index 883739dc..fc59977a 100644 --- a/workflows/phaseimpute/tests/test_quilt.nf.test.snap +++ b/workflows/phaseimpute/tests/test_quilt.nf.test.snap @@ -1,4 +1,679 @@ { + "Check test_quilt - without chunks": { + "content": [ + { + "workflow size": 24, + "versions": { + "BAMCHREXTRACT": { + "samtools": 1.23 + }, + "BCFTOOLS_CONCAT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_PLUGINSPLIT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_QUERY_IMPUTED": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_STATS_TOOLS": { + "bcftools": "1.23.1" + }, + "BGZIP_POSFILE_IMPUTE": { + "tabix": 1.21 + }, + "GAWK_IMPUTED": { + "gawk": "5.3.1" + }, + "GAWK_POSFILE_IMPUTE": { + "gawk": "5.3.1" + }, + "GLIMPSE2_LIGATE": { + "glimpse2": "2.0.0" + }, + "LISTTOFILE": { + "gawk": "5.3.1" + }, + "QUILT_QUILT": { + "r-base": "4.3.1", + "r-quilt": "1.0.5" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.23.1" + }, + "TABIX_TABIX": { + "tabix": 1.21 + }, + "Workflow": { + "nf-core/phaseimpute": "v1.2.0dev" + } + }, + "stable name": [ + "imputation", + "imputation/batch", + "imputation/batch/all_samples.batch0.id.txt", + "imputation/batch/all_samples.batch0.idonly.txt", + "imputation/batch/all_samples.batch0.noid.txt", + "imputation/csv", + "imputation/csv/impute.csv", + "imputation/quilt", + "imputation/quilt/concat", + "imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz", + "imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz.tbi", + "imputation/quilt/samples", + "imputation/quilt/samples/NA12878.quilt.vcf.gz", + "imputation/quilt/samples/NA12878.quilt.vcf.gz.tbi", + "imputation/quilt/samples/NA19401.quilt.vcf.gz", + "imputation/quilt/samples/NA19401.quilt.vcf.gz.tbi", + "imputation/quilt/samples/NA20359.quilt.vcf.gz", + "imputation/quilt/samples/NA20359.quilt.vcf.gz.tbi", + "imputation/quilt/variant_calling", + "imputation/quilt/variant_calling/RData", + "imputation/quilt/variant_calling/all_samples.batch0.chr21.quilt.ligate.vcf.gz", + "imputation/quilt/variant_calling/all_samples.batch0.chr21.quilt.ligate.vcf.gz.tbi", + "imputation/quilt/variant_calling/all_samples.batch0.chr21_16570000-16610000.quilt.vcf.gz", + "imputation/quilt/variant_calling/all_samples.batch0.chr21_16570000-16610000.quilt.vcf.gz.tbi", + "imputation/quilt/variant_calling/all_samples.batch0.chr22.quilt.ligate.vcf.gz", + "imputation/quilt/variant_calling/all_samples.batch0.chr22.quilt.ligate.vcf.gz.tbi", + "imputation/quilt/variant_calling/all_samples.batch0.chr22_16570000-16610000.quilt.vcf.gz", + "imputation/quilt/variant_calling/all_samples.batch0.chr22_16570000-16610000.quilt.vcf.gz.tbi", + "imputation/stats", + "imputation/stats/NA12878.quilt.bcftools_stats.txt", + "imputation/stats/NA19401.quilt.bcftools_stats.txt", + "imputation/stats/NA20359.quilt.bcftools_stats.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_bcftools_stats.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-cnt.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-log.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-log.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + 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"bcftools_stats_vqc_Count_Indels.txt:md5,b824aec68c806e9a55a30dc28e3df6ef", + "bcftools_stats_vqc_Count_SNP.txt:md5,be332d2de2807101988e344fc5280086", + "bcftools_stats_vqc_Count_Transitions.txt:md5,007b7ac097fc7d06b1c7e4a7b29865aa", + "bcftools_stats_vqc_Count_Transversions.txt:md5,37fa486beefe0b4d08410966898e9b45", + "multiqc_bcftools_stats.txt:md5,d4b06f92c73ef70b26e0bc448d2e28ae", + "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b", + "multiqc_general_stats.txt:md5,ca0be109c548005ec711fd5b7fcb1655" + ], + "BAM files": [ + + ], + "VCF files": [ + [ + "all_samples.batch0.quilt.vcf.gz", + "1a0d4125290fd1783048211b5657cf27" + ], + [ + "NA12878.quilt.vcf.gz", + "281e8b36038664ff1ee3c4cc6f188aa7" + ], + [ + "NA19401.quilt.vcf.gz", + "621bdd8382c62dd5302d482124035c47" + ], + [ + "NA20359.quilt.vcf.gz", + "b9a0759000a772e621bc0395a4c3df57" + ], + [ + "all_samples.batch0.chr21.quilt.ligate.vcf.gz", + "3242934ea328493b86aa221096d3a07d" + ], + [ + "all_samples.batch0.chr21_16570070-16595525.quilt.vcf.gz", + "75185b257b3b2935112af967c2891b36" + ], + [ + "all_samples.batch0.chr21_16585483-16609998.quilt.vcf.gz", + "b8b9622343f731c887b237825270e70e" + ], + [ + "all_samples.batch0.chr22.quilt.ligate.vcf.gz", + "cebbdefcd564787e030850e92cbe27de" + ], + [ + "all_samples.batch0.chr22_16570065-16597215.quilt.vcf.gz", + "26ac04b92290c3d48eaa222f9528d388" + ], + [ + "all_samples.batch0.chr22_16587172-16609999.quilt.vcf.gz", + "764af415880744e152419a9017d17054" + ] + ], + "CSV files": [ + { + "fileName": "impute.csv", + "rows": [ + "sample,tools,file,index", + "NA12878,quilt,NA12878.quilt.vcf.gz,NA12878.quilt.vcf.gz.tbi", + "NA19401,quilt,NA19401.quilt.vcf.gz,NA19401.quilt.vcf.gz.tbi", + "NA20359,quilt,NA20359.quilt.vcf.gz,NA20359.quilt.vcf.gz.tbi" + ] + } + ] + }, + { + "all_samples.batch0.quilt": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", + "samples": [ + "NA12878", + "NA19401", + "NA20359" + ] + } + } + ], + "timestamp": "2026-04-12T20:36:18.881604804", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Check test_quilt - no chunks - no map": { "content": [ { @@ -8,19 +683,19 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { "tabix": "1.21" @@ -42,7 +717,7 @@ "r-quilt": "1.0.5" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -141,9 +816,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.quilt.bcftools_stats.txt:md5,06be906390f87548cff77877dff5c981", - "NA19401.quilt.bcftools_stats.txt:md5,eaf59f02e81aeaafdc1953e92687d5d0", - "NA20359.quilt.bcftools_stats.txt:md5,24972d94b67f8d0bcfe88fa052c1f279", + "NA12878.quilt.bcftools_stats.txt:md5,ca99e46fc6a4b76ee47396b07664f861", + "NA19401.quilt.bcftools_stats.txt:md5,17f18a5af11c51c902511588b96e0482", + "NA20359.quilt.bcftools_stats.txt:md5,0905fc06908d4482a5f06e11a04a8ffb", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,21bcf26940e91c117b1b35f5dff864d6", @@ -231,19 +906,19 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { "tabix": "1.21" @@ -270,7 +945,7 @@ "r-quilt": "1.0.5" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -382,9 +1057,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.quilt.bcftools_stats.txt:md5,06be906390f87548cff77877dff5c981", - "NA19401.quilt.bcftools_stats.txt:md5,eaf59f02e81aeaafdc1953e92687d5d0", - "NA20359.quilt.bcftools_stats.txt:md5,24972d94b67f8d0bcfe88fa052c1f279", + "NA12878.quilt.bcftools_stats.txt:md5,ca99e46fc6a4b76ee47396b07664f861", + "NA19401.quilt.bcftools_stats.txt:md5,17f18a5af11c51c902511588b96e0482", + "NA20359.quilt.bcftools_stats.txt:md5,0905fc06908d4482a5f06e11a04a8ffb", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", diff --git a/workflows/phaseimpute/tests/test_quilt2.nf.test.snap b/workflows/phaseimpute/tests/test_quilt2.nf.test.snap index d436be73..897f2e0a 100644 --- a/workflows/phaseimpute/tests/test_quilt2.nf.test.snap +++ b/workflows/phaseimpute/tests/test_quilt2.nf.test.snap @@ -8,19 +8,19 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "GAWK_IMPUTED": { "gawk": "5.3.1" @@ -36,7 +36,7 @@ "r-quilt": "2.0.4" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -142,9 +142,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.quilt2.bcftools_stats.txt:md5,f88efb8027ebd4d183f07b4c3c6c8b41", - "NA19401.quilt2.bcftools_stats.txt:md5,7fd7ee760998b4b0bcff08a9a42e663b", - "NA20359.quilt2.bcftools_stats.txt:md5,06d4bf7b5c0ea4da43ecf2f65d3d78c2", + "NA12878.quilt2.bcftools_stats.txt:md5,764240dc8d060a232cc2f9e1d048a3fb", + "NA19401.quilt2.bcftools_stats.txt:md5,319fec13929c123e74dac0db2186b468", + "NA20359.quilt2.bcftools_stats.txt:md5,593343e7b2ae9b51bc7774095c6cb0da", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,46f8e72c54af931bec43d50346e6c245", @@ -225,7 +225,7 @@ } } ], - "timestamp": "2026-05-17T13:53:43.556030062", + "timestamp": "2026-05-19T16:10:06.835032331", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -240,19 +240,19 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "CUSTOM_GENETICMAPCONVERT": { "r-base": "4.5.3", @@ -273,7 +273,7 @@ "r-quilt": "2.0.4" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -384,9 +384,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.quilt2.bcftools_stats.txt:md5,f88efb8027ebd4d183f07b4c3c6c8b41", - "NA19401.quilt2.bcftools_stats.txt:md5,7fd7ee760998b4b0bcff08a9a42e663b", - "NA20359.quilt2.bcftools_stats.txt:md5,06d4bf7b5c0ea4da43ecf2f65d3d78c2", + "NA12878.quilt2.bcftools_stats.txt:md5,764240dc8d060a232cc2f9e1d048a3fb", + "NA19401.quilt2.bcftools_stats.txt:md5,319fec13929c123e74dac0db2186b468", + "NA20359.quilt2.bcftools_stats.txt:md5,593343e7b2ae9b51bc7774095c6cb0da", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", @@ -467,7 +467,7 @@ } } ], - "timestamp": "2026-05-17T15:50:32.683959431", + "timestamp": "2026-05-19T16:11:28.782157639", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -482,19 +482,19 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX": { "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "CUSTOM_GENETICMAPCONVERT": { "r-base": "4.5.3", @@ -515,7 +515,7 @@ "r-quilt": "2.0.4" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "TABIX_TABIX": { "tabix": "1.21" @@ -630,9 +630,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.quilt2.bcftools_stats.txt:md5,f88efb8027ebd4d183f07b4c3c6c8b41", - "NA19401.quilt2.bcftools_stats.txt:md5,7fd7ee760998b4b0bcff08a9a42e663b", - "NA20359.quilt2.bcftools_stats.txt:md5,06d4bf7b5c0ea4da43ecf2f65d3d78c2", + "NA12878.quilt2.bcftools_stats.txt:md5,764240dc8d060a232cc2f9e1d048a3fb", + "NA19401.quilt2.bcftools_stats.txt:md5,319fec13929c123e74dac0db2186b468", + "NA20359.quilt2.bcftools_stats.txt:md5,593343e7b2ae9b51bc7774095c6cb0da", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", @@ -721,7 +721,7 @@ } } ], - "timestamp": "2026-05-17T15:47:44.884305878", + "timestamp": "2026-05-19T16:08:39.594192642", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/phaseimpute/tests/test_sim.nf.test.snap b/workflows/phaseimpute/tests/test_sim.nf.test.snap index eb491301..cc8e0504 100644 --- a/workflows/phaseimpute/tests/test_sim.nf.test.snap +++ b/workflows/phaseimpute/tests/test_sim.nf.test.snap @@ -17,25 +17,25 @@ "gawk": "5.3.1" }, "SAMTOOLS_COVERAGE_DWN": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_COVERAGE_INP": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_DEPTH": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_INDEX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_MERGE": { - "samtools": "1.23" + "samtools": "1.23.1" }, "SAMTOOLS_VIEW": { - "samtools": "1.23" + "samtools": "1.23.1" }, "Workflow": { "nf-core/phaseimpute": "v1.2.0dev" @@ -215,10 +215,10 @@ ] } ], - "timestamp": "2026-03-30T12:23:52.713432934", + "timestamp": "2026-04-14T12:32:03.943680779", "meta": { - "nf-test": "0.9.4", - "nextflow": "26.03.1" + "nf-test": "0.9.5", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/workflows/phaseimpute/tests/test_stitch.nf.test.snap b/workflows/phaseimpute/tests/test_stitch.nf.test.snap index 1820c115..b5538374 100644 --- a/workflows/phaseimpute/tests/test_stitch.nf.test.snap +++ b/workflows/phaseimpute/tests/test_stitch.nf.test.snap @@ -8,7 +8,7 @@ "samtools": "1.23" }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -17,13 +17,13 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { "tabix": "1.21" @@ -46,7 +46,7 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "STITCH": { "r-base": "4.4.2", @@ -149,9 +149,9 @@ "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.stitch.bcftools_stats.txt:md5,6991969d019398e8704ea4cb269a315b", - "NA19401.stitch.bcftools_stats.txt:md5,2370cce588665aa328b941a0bd1a847e", - "NA20359.stitch.bcftools_stats.txt:md5,752a126486b629de8a34f826ade67086", + "NA12878.stitch.bcftools_stats.txt:md5,24d54d3ffba3fed39f7824abbf9a7d81", + "NA19401.stitch.bcftools_stats.txt:md5,360b697eac096a9b0ae2cc1059659418", + "NA20359.stitch.bcftools_stats.txt:md5,6d62a564c7fead78240007ac90bc8e3b", "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", @@ -222,16 +222,16 @@ "nextflow": "26.04.0" } }, - "Check test_stitch - no chunks - no map": { + "Check test_stitch - without chunks": { "content": [ { "workflow size": 26, "versions": { "BAMCHREXTRACT": { - "samtools": "1.23" + "samtools": 1.23 }, "BCFTOOLS_CONCAT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_INDEX_LIGATE": { "bcftools": "1.23.1" @@ -240,16 +240,16 @@ "bcftools": "1.23.1" }, "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.22" + "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { - "tabix": "1.21" + "tabix": 1.21 }, "GAWK_IMPUTED": { "gawk": "5.3.1" @@ -264,7 +264,7 @@ "gawk": "5.3.1" }, "SAMTOOLS_FAIDX": { - "samtools": "1.23" + "samtools": "1.23.1" }, "STITCH": { "r-base": "4.4.2", @@ 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