+++ /dev/null
-cwlVersion: v1.1
-class: Workflow
-
-requirements:
- - class: SubworkflowFeatureRequirement
-
-inputs:
- fastq1: File
- fastq2: File
- reference:
- type: File
- secondaryFiles:
- - .amb
- - .ann
- - .bwt
- - .pac
- - .sa
- - .fai
- - ^.dict
- sample: string
-
-outputs:
- qc-html:
- type: File[]
- outputSource: fastqc/out-html
- qc-zip:
- type: File[]
- outputSource: fastqc/out-zip
- vcf:
- type: File
- outputSource: haplotypecaller/vcf
-
-steps:
- fastqc:
- run: fastqc.cwl
- in:
- fastq1: fastq1
- fastq2: fastq2
- out: [out-html, out-zip]
- bwamem-samtools-view:
- run: bwamem-samtools-view.cwl
- in:
- fastq1: fastq1
- fastq2: fastq2
- reference: reference
- sample: sample
- out: [bam]
- samtools-sort:
- run: samtools-sort.cwl
- in:
- bam: bwamem-samtools-view/bam
- sample: sample
- out: [out]
- samtools-index:
- run: samtools-index.cwl
- in:
- bam: samtools-sort/out
- out: [out]
- haplotypecaller:
- run: gatk-haplotypecaller.cwl
- in:
- reference: reference
- bam: samtools-index/out
- sample: sample
- out: [vcf]
outputSource: generate-report/report
steps:
fastqc:
- run: fastqc.cwl
+ run: ./helper/fastqc.cwl
in:
fastq1: fastq1
fastq2: fastq2
sample: sample
out: [bam]
samtools-sort:
- run: samtools-sort.cwl
+ run: ./helper/samtools-sort.cwl
in:
bam: bwamem-samtools-view/bam
sample: sample
out: [sortedbam]
mark-duplicates:
- run: mark-duplicates.cwl
+ run: ./helper/mark-duplicates.cwl
in:
bam: samtools-sort/sortedbam
out: [dupbam,dupmetrics]
bam: mark-duplicates/dupbam
out: [indexedbam]
haplotypecaller:
- run: scatter-gatk-wf-with-interval.cwl
+ run: ./helper/scatter-gatk-wf-with-interval.cwl
in:
reference: reference
bam: samtools-index/indexedbam
knownsites1: knownsites
out: [gatheredgvcf]
generate-report:
- run: report-wf.cwl
+ run: ./helper/report-wf.cwl
in:
gvcf: haplotypecaller/gatheredgvcf
samplename: sample
reportfunc: reportfunc
headhtml: headhtml
tailhtml: tailhtml
- out: [report]
+ out: [report]
steps:
basecalibrator:
- run: gatk-baserecalibrator-with-interval.cwl
+ run: ./helper/gatk-baserecalibrator-with-interval.cwl
in:
bam: bam
reference: reference
intervallist: intervallist
out: [recaltable]
applyBQSR:
- run: gatk-applyBSQR-with-interval.cwl
+ run: ./helper/gatk-applyBSQR-with-interval.cwl
in:
reference: reference
bam: bam
recaltable: basecalibrator/recaltable
out: [recalbam]
haplotypecaller:
- run: gatk-haplotypecaller-with-interval.cwl
+ run: ./helper/gatk-haplotypecaller-with-interval.cwl
in:
reference: reference
bam: applyBQSR/recalbam
intervallist: intervallist
out: [gvcf]
selectvariants:
- run: gatk-selectvariants.cwl
+ run: ./helper/gatk-selectvariants.cwl
in:
gvcf: haplotypecaller/gvcf
reference: reference
steps:
gvcf-to-vcf:
- run: gvcf-to-vcf.cwl
+ run: ./helper/gvcf-to-vcf.cwl
in:
gvcf: gvcf
samplename: samplename
out: [vcf]
annotate:
- run: annotate-vcf.cwl
+ run: ./helper/annotate-vcf.cwl
in:
vcf: gvcf-to-vcf/vcf
clinvarvcf: clinvarvcf
out: [reporttxt]
generate-report:
- run: generate-report.cwl
+ run: ./helper/generate-report.cwl
in:
reportfunc: reportfunc
sampletxt: annotate/reporttxt
-cwlVersion: v1.1
+Version: v1.1
class: Workflow
requirements: