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fix mutect2 sample name reheader #38

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fix mutect2 sample name reheader #38

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81015ce
Generate sample identifiers from manifest fields
iamh2o Aug 26, 2025
89a61f8
X
Aug 26, 2025
4b69add
Merge pull request #27 from Daylily-Informatics/codex/refactor-analys…
iamh2o Sep 9, 2025
d76bbee
X
Sep 9, 2025
79f7a96
x
Sep 9, 2025
9acdf55
Add strelka2 variant caller rules
iamh2o Sep 9, 2025
86a953e
Add chromosome chunking for Strelka2
iamh2o Sep 9, 2025
e039229
goteam
Sep 9, 2025
4b403c2
Merge pull request #30 from Daylily-Informatics/codex/add-snakemake-r…
iamh2o Sep 9, 2025
d511d07
fix mutect2 sample name reheader
iamh2o Sep 9, 2025
e6f4e6b
x
Sep 9, 2025
95dafbc
x
Sep 9, 2025
d072d70
x
Sep 9, 2025
cf8acf0
x
Sep 9, 2025
f3c2133
x
Sep 9, 2025
bbec76e
x
Sep 9, 2025
7621faa
Merge branch 'main' into codex/fix-bam-sample-name-correction-in-mute…
iamh2o Sep 9, 2025
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6 changes: 3 additions & 3 deletions .test_data/data/0.01x_3_wgs_HG002_hg38.samplesheet.csv
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@@ -1,4 +1,4 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.95
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.85
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.75
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19,0.95
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19,0.85
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,na,HG002,HG002,NOVASEQ,PCR-FREE,19,0.75
2 changes: 1 addition & 1 deletion .test_data/data/0.01xwgs_HG002_b37.samplesheet.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
2 changes: 1 addition & 1 deletion .test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
14 changes: 7 additions & 7 deletions .test_data/data/giab_30x_b37_analysis_manifest.csv
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,na,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,na,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,na,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,na,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,na,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,na,HG007,NOVASEQ,PCR-FREE,19
14 changes: 7 additions & 7 deletions .test_data/data/giab_30x_hg38_analysis_manifest.csv
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,na,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,na,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,na,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,na,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,na,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,na,HG007,NOVASEQ,PCR-FREE,19
4 changes: 3 additions & 1 deletion config/day_profiles/local/templates/rule_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ valid_biome: AWSPC

# ###### Tool Selection CONFIG ----------------------------------------

# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe'] dedupers=['dppl'] snv_callers=['oct','clair3','deep','sentd','lfq2'] sv_callers=['manta','tiddit','dysgu']
# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe'] dedupers=['dppl'] snv_callers=['oct','clair3','deep','sentd','lfq2','strelka2'] sv_callers=['manta','tiddit','dysgu']
# and will override these defaults

# Or you can set them here
Expand Down Expand Up @@ -196,6 +196,7 @@ deepsomatic:
numa: " OMP_NUM_THREADS=8 OMP_PROC_BIND=close OMP_PLACES=threads OMP_PROC_BIND=TRUE OMP_DYNAMIC=TRUE OMP_MAX_ACTIVE_LEVELS=1 OMP_SCHEDULE=dynamic OMP_WAIT_POLICY=ACTIVE "
dvsom_conda: "../envs/vanilla_v0.1.yaml"


mutect2:
threads: 7
container: "docker://broadinstitute/gatk:4.5.0.0"
Expand All @@ -208,6 +209,7 @@ mutect2:
numa: ""
conda: "../envs/vanilla_v0.1.yaml"


duphold:
threads: 7
env_yaml: "../envs/duphold_v0.1.yaml"
Expand Down
3 changes: 2 additions & 1 deletion config/day_profiles/slurm/templates/rule_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ valid_biome: AWSPC

# ###### Tool Selection CONFIG ----------------------------------------

# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe'] dedupers=['dppl'] snv_callers=['oct','clair3','deep','sentd','lfq2'] sv_callers=['manta','tiddit','dysgu']
# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe'] dedupers=['dppl'] snv_callers=['oct','clair3','deep','sentd','lfq2','strelka2'] sv_callers=['manta','tiddit','dysgu']

# and will override these defaults

Expand Down Expand Up @@ -209,6 +209,7 @@ mutect2:




duphold:
threads: 32
env_yaml: "../envs/duphold_v0.1.yaml"
Expand Down
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