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Merged
sivkovic merged 5 commits into from
Mar 23, 2026
Merged

Hotfix/xs heme snp template #1503

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c3a9ecc
Update snps_and_indels.py
buehlere Mar 23, 2026
e85bb60
Update input_template.json.jinja2
buehlere Mar 23, 2026
c064081
Update input_template.json.jinja2
buehlere Mar 23, 2026
dbf6ba0
Merge branch 'master' into hotfix/xs_heme_snp_template
buehlere Mar 23, 2026
6240200
Update __init__.py
buehlere Mar 23, 2026
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2 changes: 1 addition & 1 deletion beagle/__init__.py
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@@ -1 +1 @@
__version__ = "2.1.1"
__version__ = "2.1.2"
179 changes: 88 additions & 91 deletions runner/operator/access/heme/snps_and_indels/input_template.json.jinja2
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@@ -1,139 +1,136 @@
{
"version": "1.3.40",
"project_name": "access_legacy_snv_pipeline",

"tumor_bams": {{ tumor_bams }},
"normal_bams": {{ normal_bams }},
"tumor_sample_names": {{ tumor_sample_names }},
"normal_sample_names": {{ normal_sample_names }},
"matched_normal_ids": {{ matched_normal_ids }},
"genotyping_bams": {{ genotyping_bams }},
"genotyping_bams_ids": {{ genotyping_bams_ids }},

"tumor_bams": {{tumor_bams}},
"normal_bams": {{normal_bams}},
"tumor_sample_names": {{tumor_sample_names}},
"normal_sample_names": {{normal_sample_names}},
"matched_normal_ids": {{matched_normal_ids}},
"genotyping_bams": {{genotyping_bams}},
"genotyping_bams_ids": {{genotyping_bams_ids}},
"mutect_params": {
"dcov": 5000,
"read_filter": ["BadCigar"],
"fraction_contamination": 0.0005,
"minimum_mutation_cell_fraction": 0.0005
"dcov": 5000,
"read_filter": ["BadCigar"],
"fraction_contamination": 0.0005,
"minimum_mutation_cell_fraction": 0.0005,
},
"vardict_params": {
"allele_freq_thres": 0.0002,
"min_num_variant_reads": 1,
"column_for_region_end": 3,
"column_for_chromosome": 1,
"column_for_gene_name": 4,
"column_for_region_start": 2
"allele_freq_thres": 0.0002,
"min_num_variant_reads": 1,
"column_for_region_end": 3,
"column_for_chromosome": 1,
"column_for_gene_name": 4,
"column_for_region_start": 2,
},
"basicfiltering_mutect_params": {
"total_depth": 20,
"allele_depth": 1,
"variant_fraction": 0.00005,
"tumor_normal_ratio": 1,
"outdir": "."
"total_depth": 20,
"allele_depth": 1,
"variant_fraction": 0.00005,
"tumor_normal_ratio": 1,
"outdir": ".",
},
"basicfiltering_vardict_params": {
"min_qual": 0,
"total_depth": 20,
"allele_depth": 1,
"tumor_normal_ratio": 1,
"filter_germline": false,
"variant_fraction": 0.00005,
"outdir": "."
},
"bcftools_params": {
"allow_overlaps": true,
"rm_dups": "none"
},
"min_qual": 0,
"total_depth": 20,
"allele_depth": 1,
"tumor_normal_ratio": 1,
"filter_germline": false,
"variant_fraction": 0.00005,
"outdir": ".",
},
"bcftools_params": {"allow_overlaps": true, "rm_dups": "none"},
"vcf2maf_params": {
"vep_forks": 4,
"buffer_size": 5000,
"max_filter_ac": 10,
"min_hom_vaf": 0.7,
"ncbi_build": "GRCh37",
"retain_info": "set,TYPE,FAILURE_REASON,MUTECT,VCF_POS,VCF_REF,VCF_ALT",
"maf_center": "mskcc.org",
"species": "homo_sapiens_merged"
},
"gbcms_params": {
"maq": 20,
"thread": 10,
"omaf": true,
"fragment_count": 1,
"filter_duplicate": 0
},
"vep_forks": 4,
"buffer_size": 5000,
"max_filter_ac": 10,
"min_hom_vaf": 0.7,
"ncbi_build": "GRCh37",
"retain_info": "set,TYPE,FAILURE_REASON,MUTECT,VCF_POS,VCF_REF,VCF_ALT",
"maf_center": "mskcc.org",
"species": "homo_sapiens_merged",
},
"gbcms_params": {"maq": 20, "thread": 10, "omaf": true, "fragment_count": 1, "filter_duplicate": 0},
"access_filters_params": {
"tumor_TD_min": 20,
"normal_TD_min": 20,
"tn_ratio_thres": 2,
"tier_one_alt_min": 3,
"tier_two_alt_min": 5,
"tumor_detect_alt_thres": 2,
"curated_detect_alt_thres": 2,
"DS_tumor_detect_alt_thres": 2,
"DS_curated_detect_alt_thres": 2,
"tumor_vaf_germline_thres": 0,
"normal_vaf_germline_thres": 0.3,
"min_n_curated_samples_alt_detected": 2
"tumor_TD_min": 20,
"normal_TD_min": 20,
"tn_ratio_thres": 2,
"tier_one_alt_min": 3,
"tier_two_alt_min": 5,
"tumor_detect_alt_thres": 2,
"curated_detect_alt_thres": 2,
"DS_tumor_detect_alt_thres": 2,
"DS_curated_detect_alt_thres": 2,
"tumor_vaf_germline_thres": 0,
"normal_vaf_germline_thres": 0.3,
"min_n_curated_samples_alt_detected": 2,
},
"dbsnp": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/dbsnp_137.b37.vcf"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/dbsnp_137.b37.vcf",
},
"cosmic": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/CosmicCodingMuts_v67_b37_20131024__NDS.vcf"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/CosmicCodingMuts_v67_b37_20131024__NDS.vcf",
},
"ref_fasta": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/v20221027_viral_updates/hg19_virus.fa"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/v20221027_viral_updates/hg19_virus.fa",
},
"exac_filter": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz",
},
"hotspots": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/hotspot-list-union-v1-v2.txt"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/hotspot-list-union-v1-v2.txt",
},
"blacklist_file": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ACCESS_blacklist_20_05_2019.txt"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ACCESS_blacklist_20_05_2019.txt",
},
"heme_hotspots": {
"class": "File",
"path": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/ACCESSH_hotspots.txt",
},
"heme_tsgs": {
"class": "File",
"path": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/ACCESSH_TSGs.txt",
},
"custom_enst_file": {
"class": "File",
"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/dmp_isoform_merged_overrides.txt"
"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/dmp_isoform_merged_overrides.txt",
},
"bed_file": {
"class": "File",
"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/MSK-ACCESS-Heme-v1_canonicaltargets_500buffer.bed"
"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/MSK-ACCESS-Heme-v1_canonicaltargets_500buffer.bed",
},
"annotate_concat_header_file": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/mutect_annotate_concat_header.txt"
"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/mutect_annotate_concat_header.txt",
},
"reference_bam_for_VC": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_unmatched_VC/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam"
"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_unmatched_VC/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam",
},
"reference_bam_for_SV": {
"class": "File",
"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_SV/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR.bam"
"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_SV/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR.bam",
},
"run_tools": {
"bcftools": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools",
"gbcms": "/usersoftware/core005/access/production/V1/tools/GetBaseCountsMultiSample-1.2.5/GetBaseCountsMultiSample",
"java_7": "/admin/software/migration-testing/java/jdk1.7.0_80/bin/java",
"mutect": "/usersoftware/core005/access/production/V1/tools/muTect/versions/v1.1.5/muTect-1.1.5.jar",
"vardict": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/bin/VarDict",
"vardict_testsomatic": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/testsomatic.R",
"vardict_var2vcf_paired": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl",
"perl": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/perl",
"vcf2maf": "/usersoftware/core005/access/production/V1/tools/vcf2maf/mskcc-vcf2maf-2235eed/vcf2maf.pl",
"vep_path": "/data1/core005/assets/msk-access/v1.0/vep/v86/",
"vep_data": "/data1/core005/assets/msk-access/v1.0/vep/cache/",
"tabix": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/tabix",
"bgzip": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/bgzip",
"sortbed": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/sortBed",
"bcftools_1_6": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools"
}
"bcftools": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools",
"gbcms": "/usersoftware/core005/access/production/V1/tools/GetBaseCountsMultiSample-1.2.5/GetBaseCountsMultiSample",
"java_7": "/admin/software/migration-testing/java/jdk1.7.0_80/bin/java",
"mutect": "/usersoftware/core005/access/production/V1/tools/muTect/versions/v1.1.5/muTect-1.1.5.jar",
"vardict": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/bin/VarDict",
"vardict_testsomatic": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/testsomatic.R",
"vardict_var2vcf_paired": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl",
"perl": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/perl",
"vcf2maf": "/usersoftware/core005/access/production/V1/tools/vcf2maf/mskcc-vcf2maf-2235eed/vcf2maf.pl",
"vep_path": "/data1/core005/assets/msk-access/v1.0/vep/v86/",
"vep_data": "/data1/core005/assets/msk-access/v1.0/vep/cache/",
"tabix": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/tabix",
"bgzip": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/bgzip",
"sortbed": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/sortBed",
"bcftools_1_6": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools",
},
}
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