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Merge pull request #9 from mskcc/release_candidate/1.1.0
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1.1.0
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@allanbolipata
allanbolipata authored Sep 2, 2020
2 parents 2fc732c + d1d88a3 commit f0ed3da
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Showing 10 changed files with 67 additions and 349 deletions.
82 changes: 0 additions & 82 deletions modules/pair/facets.cwl
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77 changes: 18 additions & 59 deletions modules/pair/variant-calling-pair.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@ requirements:
inputs:
tumor_bam: File
normal_bam: File
genome: string
bed: File
normal_sample_name: string
tumor_sample_name: string
Expand All @@ -38,8 +37,6 @@ inputs:
- .sa
- .fai
- ^.dict
facets_pcval: int
facets_cval: int
facets_snps: File
complex_nn: float
complex_tn: float
Expand All @@ -52,27 +49,9 @@ outputs:
annotate_vcf:
type: File
outputSource: annotate/annotate_vcf_output_file
facets_png:
type: File[]
outputSource: call_variants/facets_png
facets_txt_hisens:
snp_pileup:
type: File
outputSource: call_variants/facets_txt_hisens
facets_txt_purity:
type: File
outputSource: call_variants/facets_txt_purity
facets_out:
type: File[]
outputSource: call_variants/facets_out
facets_rdata:
type: File[]
outputSource: call_variants/facets_rdata
facets_seg:
type: File[]
outputSource: call_variants/facets_seg
facets_counts:
type: File
outputSource: call_variants/facets_counts
outputSource: call_variants/snp_pileup
mutect_vcf:
type: File
outputSource: call_variants/mutect_vcf
Expand Down Expand Up @@ -107,7 +86,6 @@ steps:
in:
tumor_bam: tumor_index/bam_indexed
normal_bam: normal_index/bam_indexed
genome: genome
ref_fasta: ref_fasta
normal_sample_name: normal_sample_name
tumor_sample_name: tumor_sample_name
Expand All @@ -117,17 +95,14 @@ steps:
mutect_rf: mutect_rf
bed: bed
refseq: refseq
facets_pcval: facets_pcval
facets_cval: facets_cval
facets_snps: facets_snps
out: [ vardict_vcf, mutect_vcf, mutect_callstats, facets_png, facets_txt_hisens, facets_txt_purity, facets_out, facets_rdata, facets_seg, facets_counts]
out: [ vardict_vcf, mutect_vcf, mutect_callstats, snp_pileup]
run:
class: Workflow
id: call-variants
inputs:
tumor_bam: File
genome: string
normal_bam: File
tumor_bam: File
ref_fasta: File
normal_sample_name: string
tumor_sample_name: string
Expand All @@ -137,8 +112,6 @@ steps:
mutect_rf: string[]
bed: File
refseq: File #file of refseq genes...
facets_pcval: int
facets_cval: int
facets_snps: File
outputs:
mutect_vcf:
Expand All @@ -150,39 +123,25 @@ steps:
vardict_vcf:
type: File
outputSource: vardict/output
facets_png:
type: File[]
outputSource: facets/facets_png_output
facets_txt_hisens:
type: File
outputSource: facets/facets_txt_output_hisens
facets_txt_purity:
type: File
outputSource: facets/facets_txt_output_purity
facets_out:
type: File[]
outputSource: facets/facets_out_output
facets_rdata:
type: File[]
outputSource: facets/facets_rdata_output
facets_seg:
type: File[]
outputSource: facets/facets_seg_output
facets_counts:
snp_pileup:
type: File
outputSource: facets/facets_counts_output
outputSource: snp_pileup/out_file
steps:
facets:
run: facets.cwl
snp_pileup:
run: ../../tools/htstools/0.1.1/snp-pileup.cwl
in:
normal_bam: normal_bam
tumor_bam: tumor_bam
tumor_sample_name: tumor_sample_name
genome: genome
facets_pcval: facets_pcval
facets_cval: facets_cval
facets_snps: facets_snps
out: [facets_png_output, facets_txt_output_hisens, facets_txt_output_purity, facets_out_output, facets_rdata_output, facets_seg_output, facets_counts_output]
vcf: facets_snps
output_file:
valueFrom: ${ return inputs.normal_bam.basename.replace(".bam", "") + "__" + inputs.tumor_bam.basename.replace(".bam", "") + ".dat.gz"; }
count_orphans:
valueFrom: ${ return true; }
gzip:
valueFrom: ${ return true; }
pseudo_snps:
default: "50"
out: [out_file]
vardict:
run: ../../tools/vardict/1.5.1/vardict.cwl
in:
Expand Down
50 changes: 5 additions & 45 deletions project-workflow-sv.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -214,50 +214,10 @@ outputs:
outputSource: pair_process/mutect_norm_vcf
secondaryFiles:
- .tbi
# facets
facets_png:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_png
facets_txt_hisens:
type:
type: array
items: File
outputSource: pair_process/facets_txt_hisens
facets_txt_purity:
type:
type: array
items: File
outputSource: pair_process/facets_txt_purity
facets_out:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_out
facets_rdata:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_rdata
facets_seg:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_seg
facets_counts:
type:
type: array
items: File
outputSource: pair_process/facets_counts
# snp_pileup
snp_pileup:
type: File[]
outputSource: pair_process/snp_pileup
# structural variants
merged_file_unfiltered:
type: File[]
Expand Down Expand Up @@ -300,7 +260,7 @@ steps:
pair: pairs
ref_fasta: ref_fasta
mouse_fasta: mouse_fasta
out: [normal_bam,tumor_bam,clstats1,clstats2,md_metrics,as_metrics,hs_metrics,insert_metrics,insert_pdf,per_target_coverage,qual_metrics,qual_pdf,doc_basecounts,gcbias_pdf,gcbias_metrics,gcbias_summary,conpair_pileups,mutect_vcf,mutect_callstats,vardict_vcf,combine_vcf,annotate_vcf,vardict_norm_vcf,mutect_norm_vcf,facets_png,facets_txt_hisens,facets_txt_purity,facets_out,facets_rdata,facets_seg,facets_counts,merged_file_unfiltered,merged_file,maf_file,portal_file,maf,genome,assay,pi,pi_email,project_prefix,normal_sample_name,tumor_sample_name]
out: [normal_bam,tumor_bam,clstats1,clstats2,md_metrics,as_metrics,hs_metrics,insert_metrics,insert_pdf,per_target_coverage,qual_metrics,qual_pdf,doc_basecounts,gcbias_pdf,gcbias_metrics,gcbias_summary,conpair_pileups,mutect_vcf,mutect_callstats,vardict_vcf,combine_vcf,annotate_vcf,vardict_norm_vcf,mutect_norm_vcf,snp_pileup,merged_file_unfiltered,merged_file,maf_file,portal_file,maf,genome,assay,pi,pi_email,project_prefix,normal_sample_name,tumor_sample_name]
scatter: [pair]
scatterMethod: dotproduct

Expand Down
52 changes: 5 additions & 47 deletions project-workflow.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -213,56 +213,14 @@ outputs:
outputSource: pair_process/mutect_norm_vcf
secondaryFiles:
- .tbi
# facets
facets_png:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_png
facets_txt_hisens:
type:
type: array
items: File
outputSource: pair_process/facets_txt_hisens
facets_txt_purity:
type:
type: array
items: File
outputSource: pair_process/facets_txt_purity
facets_out:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_out
facets_rdata:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_rdata
facets_seg:
type:
type: array
items:
type: array
items: File
outputSource: pair_process/facets_seg
facets_counts:
type:
type: array
items: File
outputSource: pair_process/facets_counts

# snp_pileup
snp_pileup:
type: File[]
outputSource: pair_process/snp_pileup
# maf
maf:
type: File[]
outputSource: pair_process/maf

# qc
qc_pdf:
type: File
Expand All @@ -288,7 +246,7 @@ steps:
pair: pairs
ref_fasta: ref_fasta
mouse_fasta: mouse_fasta
out: [normal_bam,tumor_bam,clstats1,clstats2,md_metrics,as_metrics,hs_metrics,insert_metrics,insert_pdf,per_target_coverage,qual_metrics,qual_pdf,doc_basecounts,gcbias_pdf,gcbias_metrics,gcbias_summary,conpair_pileups,mutect_vcf,mutect_callstats,vardict_vcf,combine_vcf,annotate_vcf,vardict_norm_vcf,mutect_norm_vcf,facets_png,facets_txt_hisens,facets_txt_purity,facets_out,facets_rdata,facets_seg,facets_counts,maf,genome,assay,pi,pi_email,project_prefix,normal_sample_name,tumor_sample_name]
out: [normal_bam,tumor_bam,clstats1,clstats2,md_metrics,as_metrics,hs_metrics,insert_metrics,insert_pdf,per_target_coverage,qual_metrics,qual_pdf,doc_basecounts,gcbias_pdf,gcbias_metrics,gcbias_summary,conpair_pileups,mutect_vcf,mutect_callstats,vardict_vcf,combine_vcf,annotate_vcf,vardict_norm_vcf,mutect_norm_vcf,snp_pileup,maf,genome,assay,pi,pi_email,project_prefix,normal_sample_name,tumor_sample_name]
scatter: [pair]
scatterMethod: dotproduct

Expand Down
15 changes: 0 additions & 15 deletions test/copy_outputs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,21 +13,6 @@ maf:
path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
facets:
- normal_id: foo_normal
tumor_id: foo_tumor
files:
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_hisens.CNCF.png
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_purity.CNCF.png
- normal_id: bar_normal
tumor_id: bar_tumor
files:
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_hisens.CNCF.png
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png
meta:
- class: File
path: /juno/work/ci/argos-test/data/fastq/DU874145-N/SampleSheet.csv
Expand Down
17 changes: 1 addition & 16 deletions test/copy_outputs_without_meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,19 +12,4 @@ maf:
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
facets:
- normal_id: foo_normal
tumor_id: foo_tumor
files:
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_hisens.CNCF.png
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_purity.CNCF.png
- normal_id: bar_normal
tumor_id: bar_tumor
files:
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_hisens.CNCF.png
- class: File
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png
path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
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