Rearranging for clarity

[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
deleted file mode 100644 (file)
index 0a4b9d2..0000000
--- a/cwl/helper/bwa-gatk-report-wf.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-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]