Template update 3.5.2 by nictru · Pull Request #103 · nf-core/hadge

nictru · 2026-02-15T10:03:38Z

This also switches to the nf-core github runners, as using them is part of the nf-core template. Partly replaces #101

github-actions · 2026-02-15T10:05:37Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit d4fc618

+| ✅ 359 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  16 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-hadge_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-hadge_logo_light.png
files_exist - File found: docs/images/nf-core-hadge_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-hadge_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowHadge.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.mode= rescue
nextflow_config - Config default value correct: params.hash_tools= gmm-demux
nextflow_config - Config default value correct: params.genetic_tools= vireo
nextflow_config - Config default value correct: params.bam_qc= true
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.match_donor= true
nextflow_config - Config default value correct: params.find_variants= true
nextflow_config - Config default value correct: params.subset_gt_donors= true
nextflow_config - Config default value correct: params.variant_count= 10
nextflow_config - Config default value correct: params.variant_pct= 0.9
nextflow_config - Config default value correct: params.demuxem_generate_diagnostic_plots= true
nextflow_config - Config default value correct: params.demuxem_alpha_on_samples= 0.0
nextflow_config - Config default value correct: params.demuxem_min_num_genes= 100
nextflow_config - Config default value correct: params.demuxem_min_num_umis= 100
nextflow_config - Config default value correct: params.demuxem_min_signal_hashtag= 10.0
nextflow_config - Config default value correct: params.demuxem_random_state= 0
nextflow_config - Config default value correct: params.bff_methods= COMBINED
nextflow_config - Config default value correct: params.bff_preprocessing= true
nextflow_config - Config default value correct: params.bff_doHeatmap= true
nextflow_config - Config default value correct: params.bff_chemistry= 10xV3
nextflow_config - Config default value correct: params.gmmdemux_type_report= true
nextflow_config - Config default value correct: params.gmmdemux_summary_report= true
nextflow_config - Config default value correct: params.gmmdemux_threshold= 0.8
nextflow_config - Config default value correct: params.gmmdemux_random_state= 0
nextflow_config - Config default value correct: params.hashsolo_priors= 0.01,0.8,0.19
nextflow_config - Config default value correct: params.hashsolo_round_digits= 10
nextflow_config - Config default value correct: params.htodemux_quantile= 0.99
nextflow_config - Config default value correct: params.htodemux_init= NULL
nextflow_config - Config default value correct: params.htodemux_nstarts= 100
nextflow_config - Config default value correct: params.htodemux_kfunc= clara
nextflow_config - Config default value correct: params.htodemux_nsamples= 100
nextflow_config - Config default value correct: params.htodemux_seed= 42
nextflow_config - Config default value correct: params.htodemux_verbose= true
nextflow_config - Config default value correct: params.htodemux_visualization_ridgePlot= true
nextflow_config - Config default value correct: params.htodemux_visualization_ridgeNCol= 2
nextflow_config - Config default value correct: params.htodemux_visualization_featureScatter= true
nextflow_config - Config default value correct: params.htodemux_visualization_vlnPlot= true
nextflow_config - Config default value correct: params.htodemux_visualization_vlnFeatures= nCount_RNA
nextflow_config - Config default value correct: params.htodemux_visualization_vlnLog= true
nextflow_config - Config default value correct: params.htodemux_visualization_tSNE= true
nextflow_config - Config default value correct: params.htodemux_visualization_tSNEIdents= Negative
nextflow_config - Config default value correct: params.htodemux_visualization_tSNEInvert= true
nextflow_config - Config default value correct: params.htodemux_visualization_tSNEDimMax= 2
nextflow_config - Config default value correct: params.htodemux_visualization_tSNEPerplexity= 100
nextflow_config - Config default value correct: params.htodemux_visualization_heatMap= true
nextflow_config - Config default value correct: params.htodemux_visualization_heatMapNcells= 500
nextflow_config - Config default value correct: params.multiseqdemux_quantile= 0.7
nextflow_config - Config default value correct: params.multiseqdemux_autoThresh= true
nextflow_config - Config default value correct: params.multiseqdemux_maxiter= 5
nextflow_config - Config default value correct: params.multiseqdemux_qrangeFrom= 0.1
nextflow_config - Config default value correct: params.multiseqdemux_qrangeTo= 0.9
nextflow_config - Config default value correct: params.multiseqdemux_qrangeBy= 0.05
nextflow_config - Config default value correct: params.multiseqdemux_verbose= true
nextflow_config - Config default value correct: params.hasheddrops_lower= 100
nextflow_config - Config default value correct: params.hasheddrops_niters= 10000
nextflow_config - Config default value correct: params.hasheddrops_testAmbient= true
nextflow_config - Config default value correct: params.hasheddrops_round= true
nextflow_config - Config default value correct: params.hasheddrops_isCellFDR= 0.01
nextflow_config - Config default value correct: params.hasheddrops_gene_col= 2
nextflow_config - Config default value correct: params.hasheddrops_ambient= true
nextflow_config - Config default value correct: params.hasheddrops_minProp= 0.05
nextflow_config - Config default value correct: params.hasheddrops_pseudoCount= 5
nextflow_config - Config default value correct: params.hasheddrops_doubletNmads= 3
nextflow_config - Config default value correct: params.hasheddrops_doubletMin= 2
nextflow_config - Config default value correct: params.hasheddrops_confidentNmads= 3
nextflow_config - Config default value correct: params.hasheddrops_confidentMin= 2
nextflow_config - Config default value correct: params.preprocessing_sel_method= mean.var.plot
nextflow_config - Config default value correct: params.preprocessing_ndelim= _
nextflow_config - Config default value correct: params.preprocessing_n_features= 2000
nextflow_config - Config default value correct: params.preprocessing_assay= HTO
nextflow_config - Config default value correct: params.preprocessing_margin= 2
nextflow_config - Config default value correct: params.preprocessing_norm_method= CLR
nextflow_config - Config default value correct: params.preprocessing_gene_col= 2
nextflow_config - Config default value correct: params.generate_anndata= true
nextflow_config - Config default value correct: params.generate_mudata= true
nextflow_config - Config default value correct: params.cellsnp_celltag= CB
nextflow_config - Config default value correct: params.cellsnp_umitag= Auto
nextflow_config - Config default value correct: params.cellsnp_mincount= 20
nextflow_config - Config default value correct: params.cellsnp_minmaf= 0.0
nextflow_config - Config default value correct: params.cellsnp_minlen= 30
nextflow_config - Config default value correct: params.cellsnp_minmapq= 20
nextflow_config - Config default value correct: params.cellsnp_maxdepth= 0
nextflow_config - Config default value correct: params.vireo_genotag= GT
nextflow_config - Config default value correct: params.vireo_n_init= 50
nextflow_config - Config default value correct: params.vireo_extra_donor= 0
nextflow_config - Config default value correct: params.vireo_extra_donor_mode= distance
nextflow_config - Config default value correct: params.vireo_force_learn_gt= true
nextflow_config - Config default value correct: params.vireo_rand_seed= 0
nextflow_config - Config default value correct: params.vireo_cell_range= all
nextflow_config - Config default value correct: params.dsc_pileup_tag_group= CB
nextflow_config - Config default value correct: params.dsc_pileup_tag_umi= UB
nextflow_config - Config default value correct: params.dsc_pileup_cap_bq= 40
nextflow_config - Config default value correct: params.dsc_pileup_min_bq= 13
nextflow_config - Config default value correct: params.dsc_pileup_min_mq= 20
nextflow_config - Config default value correct: params.dsc_pileup_min_td= 0
nextflow_config - Config default value correct: params.dsc_pileup_excl_flag= 3844
nextflow_config - Config default value correct: params.dsc_pileup_min_total= 0
nextflow_config - Config default value correct: params.dsc_pileup_min_uniq= 0
nextflow_config - Config default value correct: params.dsc_pileup_min_snp= 0
nextflow_config - Config default value correct: params.demuxlet_field= GT
nextflow_config - Config default value correct: params.demuxlet_geno_error_offset= 0.1
nextflow_config - Config default value correct: params.demuxlet_geno_error_coeff= 0.0
nextflow_config - Config default value correct: params.demuxlet_r2_info= R2
nextflow_config - Config default value correct: params.demuxlet_min_mac= 1
nextflow_config - Config default value correct: params.demuxlet_min_callrate= 0.5
nextflow_config - Config default value correct: params.demuxlet_alpha= 0.1,0.2,0.3,0.4,0.5
nextflow_config - Config default value correct: params.demuxlet_doublet_prior= 0.5
nextflow_config - Config default value correct: params.freemuxlet_doublet_prior= 0.5
nextflow_config - Config default value correct: params.freemuxlet_geno_error= 0.1
nextflow_config - Config default value correct: params.freemuxlet_bf_thres= 5.41
nextflow_config - Config default value correct: params.freemuxlet_frac_init_clust= 1.0
nextflow_config - Config default value correct: params.freemuxlet_iter_init= 10
nextflow_config - Config default value correct: params.freemuxlet_seed= 0
nextflow_config - Config default value correct: params.souporcell_ploidy= 2
nextflow_config - Config default value correct: params.souporcell_min_alt= 10
nextflow_config - Config default value correct: params.souporcell_min_ref= 10
nextflow_config - Config default value correct: params.souporcell_max_loci= 2048
nextflow_config - Config default value correct: params.souporcell_restarts= 100
nextflow_config - Config default value correct: params.souporcell_skip_remap= false
nextflow_config - Config default value correct: params.souporcell_ignore= false
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_donor_match.nf.test' contains outdir parameter
nf_test_content - 'tests/test_donor_match.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_donor_match.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_hashing.nf.test' contains outdir parameter
nf_test_content - 'tests/test_hashing.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_hashing.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_genetic.nf.test' contains outdir parameter
nf_test_content - 'tests/test_genetic.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_genetic.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-hadge_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hadge_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hadge_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - UMITOOLS_DEDUP found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_HASHES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BAM found in conf/modules.config and Nextflow scripts.
modules_config - DONOR_MATCH found in conf/modules.config and Nextflow scripts.
modules_config - FIND_VARIANTS found in conf/modules.config and Nextflow scripts.
modules_config - SUBSET_GT_DONORS found in conf/modules.config and Nextflow scripts.
modules_config - JOIN_RESULTS_ASSIGNMENT found in conf/modules.config and Nextflow scripts.
modules_config - JOIN_RESULTS_CLASSIFICATION found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ANNDATA_MUDATA found in conf/modules.config and Nextflow scripts.
modules_config - CELLSNP_MODEA found in conf/modules.config and Nextflow scripts.
modules_config - VIREO found in conf/modules.config and Nextflow scripts.
modules_config - POPSCLE_DSCPILEUP found in conf/modules.config and Nextflow scripts.
modules_config - POPSCLE_DEMUXLET found in conf/modules.config and Nextflow scripts.
modules_config - POPSCLE_FREEMUXLET found in conf/modules.config and Nextflow scripts.
modules_config - SOUPORCELL found in conf/modules.config and Nextflow scripts.
modules_config - MTXCONVERT_RNA found in conf/modules.config and Nextflow scripts.
modules_config - MTXCONVERT_HTO found in conf/modules.config and Nextflow scripts.
modules_config - DEMUXEM found in conf/modules.config and Nextflow scripts.
modules_config - BFF found in conf/modules.config and Nextflow scripts.
modules_config - GMMDEMUX found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_RNA found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_HTO found in conf/modules.config and Nextflow scripts.
modules_config - HTODEMUX found in conf/modules.config and Nextflow scripts.
modules_config - HTODEMUX_VISUALIZATION found in conf/modules.config and Nextflow scripts.
modules_config - MULTISEQDEMUX found in conf/modules.config and Nextflow scripts.
modules_config - HASHEDDROPS found in conf/modules.config and Nextflow scripts.
modules_config - HASH_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - GENE_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - PREPROCESSING_FOR_HTODEMUX_MULTISEQ found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_HASHSOLO found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-02-20 16:36:53

LuisHeinzlmeier

I only noticed the difference in the capitalization of Channel. Other than that, LGTM. Thank you @nictru!

LuisHeinzlmeier · 2026-02-20T16:36:59Z

Changed all uppercase Channels to lowercase channels (except for nf-core modules).

nictru · 2026-02-20T18:17:37Z

You can change your review to merge it, I can't approve my own PR

nictru added 4 commits September 16, 2025 19:36

Template update for nf-core/tools version 3.3.2

9518966

Template update for nf-core/tools version 3.3.2

c9e653d

Template update for nf-core/tools version 3.5.2

c81afb0

Merge branch 'TEMPLATE' into template-update-3.5.2

60e27ea

Update multiqc

d3f7b82

nictru requested a review from LuisHeinzlmeier February 15, 2026 10:55

nictru mentioned this pull request Feb 15, 2026

Add strict syntax support #104

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LuisHeinzlmeier reviewed Feb 20, 2026

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Comment thread workflows/hadge.nf

Comment thread workflows/hadge.nf

nictru enabled auto-merge (squash) February 20, 2026 13:24

LuisHeinzlmeier added 2 commits February 20, 2026 17:30

test

4aa7f55

change to lowercase channel

d4fc618

LuisHeinzlmeier self-requested a review February 22, 2026 11:07

LuisHeinzlmeier approved these changes Feb 22, 2026

View reviewed changes

nictru merged commit 067f0a1 into dev Feb 22, 2026
14 checks passed

nictru deleted the template-update-3.5.2 branch February 22, 2026 15:34

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Template update 3.5.2#103

Template update 3.5.2#103
nictru merged 7 commits intodevfrom
template-update-3.5.2

nictru commented Feb 15, 2026

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LuisHeinzlmeier commented Feb 20, 2026 •

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

LuisHeinzlmeier commented Feb 20, 2026 •

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