Adding modified code to select variants and gather arrays

[arvados-tutorial.git] / cwl / helper / bwa-gatk-report-wf.cwl

diff --git a/cwl/helper/bwa-gatk-report-wf.cwl b/cwl/helper/bwa-gatk-report-wf.cwl
new file mode 100644 (file)
index 0000000..0a4b9d2
--- /dev/null
+++ b/cwl/helper/bwa-gatk-report-wf.cwl
@@ -0,0 +1,93 @@
+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
+  knownsites:
+    type: File
+    secondaryFiles:
+      - .tbi   
+  scattercount: string
+  clinvarvcf: File
+  reportfunc: File
+  headhtml: File
+  tailhtml: File
+
+outputs:
+  qc-html:
+    type: File[]
+    outputSource: fastqc/out-html
+  qc-zip:
+    type: File[]
+    outputSource: fastqc/out-zip 
+  gvcf:
+    type: File
+    outputSource: haplotypecaller/gatheredgvcf
+  report:
+    type: File  
+    outputSource: generate-report/report
+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: [sortedbam]
+  mark-duplicates:
+    run: mark-duplicates.cwl
+    in:
+      bam: samtools-sort/sortedbam
+    out: [dupbam,dupmetrics]
+  samtools-index:
+    run: samtools-index.cwl
+    in:
+      bam: mark-duplicates/dupbam
+    out: [indexedbam]
+  haplotypecaller:
+    run: scatter-gatk-wf-with-interval.cwl 
+    in:
+      reference: reference
+      bam: samtools-index/indexedbam
+      sample: sample
+      scattercount: scattercount
+      knownsites1: knownsites
+    out: [gatheredgvcf]
+  generate-report:
+    run: report-wf.cwl
+    in:
+      gvcf: haplotypecaller/gatheredgvcf
+      samplename: sample
+      clinvarvcf: clinvarvcf
+      reportfunc: reportfunc
+      headhtml: headhtml
+      tailhtml: tailhtml
+    out: [report]