Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>

[arvados-tutorial.git] / cwl / bwamem-samtools-view.cwl

diff --git a/cwl/bwamem-samtools-view.cwl b/cwl/bwamem-samtools-view.cwl
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+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: curii/bwa-samtools-picard
+  ShellCommandRequirement: {}
+  ResourceRequirement:
+    ramMin: 26000
+    coresMin: 8
+
+arguments:
+  - /bwa-0.7.17/bwa
+  - mem
+  - -t
+  - $(runtime.cores)
+  - $(inputs.reference)
+  - -R
+  - "@RG\\tID:sample\\tSM:sample\\tLB:sample\\tPL:ILLUMINA"
+  - $(inputs.fastq1)
+  - $(inputs.fastq2)
+  - shellQuote: false
+    valueFrom: '|'
+  - samtools
+  - view
+  - -b
+  - -S
+  - shellQuote: false
+    valueFrom: '-'
+
+inputs:
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  fastq1: File
+  fastq2: File
+  sample: string
+
+stdout: $(inputs.sample).bam
+
+outputs:
+  bam:
+    type: File
+    outputBinding:
+      glob: "*bam"