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Add step to run normal bam_readcount #198

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Sep 12, 2017
Merged

Add step to run normal bam_readcount #198

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37 changes: 30 additions & 7 deletions detect_variants/detect_variants.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -122,12 +122,18 @@ outputs:
vep_summary:
type: File
outputSource: annotate_variants/vep_summary
snv_bam_readcount:
tumor_snv_bam_readcount:
type: File
outputSource: bam_readcount/snv_bam_readcount
indel_bam_readcount:
outputSource: tumor_bam_readcount/snv_bam_readcount
tumor_indel_bam_readcount:
type: File
outputSource: bam_readcount/indel_bam_readcount
outputSource: tumor_bam_readcount/indel_bam_readcount
normal_snv_bam_readcount:
type: File
outputSource: normal_bam_readcount/snv_bam_readcount
normal_indel_bam_readcount:
type: File
outputSource: normal_bam_readcount/indel_bam_readcount
steps:
mutect:
run: ../mutect/workflow.cwl
Expand Down Expand Up @@ -211,21 +217,38 @@ steps:
reference: reference
out:
[annotated_vcf, vep_summary]
cram_to_bam:
tumor_cram_to_bam:
run: ../cram_to_bam/workflow.cwl
in:
cram: tumor_cram
reference: reference
out:
[bam]
bam_readcount:
normal_cram_to_bam:
run: ../cram_to_bam/workflow.cwl
in:
cram: normal_cram
reference: reference
out:
[bam]
tumor_bam_readcount:
run: ../pvacseq/bam_readcount.cwl
in:
vcf: combine/combined_vcf
sample:
default: 'TUMOR'
reference_fasta: reference
bam: cram_to_bam/bam
bam: tumor_cram_to_bam/bam
out:
[snv_bam_readcount, indel_bam_readcount]
normal_bam_readcount:
run: ../pvacseq/bam_readcount.cwl
in:
vcf: combine/combined_vcf
sample:
default: 'NORMAL'
reference_fasta: reference
bam: normal_cram_to_bam/bam
out:
[snv_bam_readcount, indel_bam_readcount]
bgzip:
Expand Down
4 changes: 2 additions & 2 deletions pvacseq/bam_readcount.cwl
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Expand Up @@ -30,8 +30,8 @@ outputs:
snv_bam_readcount:
type: File?
outputBinding:
glob: bam_readcount_snv.tsv
glob: $(inputs.sample)_bam_readcount_snv.tsv
indel_bam_readcount:
type: File?
outputBinding:
glob: bam_readcount_indel.tsv
glob: $(inputs.sample)_bam_readcount_indel.tsv