Rearranging for clarity

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

diff --git a/cwl/helper/bwamem-samtools-view.cwl b/cwl/helper/bwamem-samtools-view.cwl
deleted file mode 100644 (file)
index 689bf39..0000000
--- a/cwl/helper/bwamem-samtools-view.cwl
+++ /dev/null
@@ -1,65 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Realigning fastqs and converting output to bam
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
-  DockerRequirement:
-    dockerPull: curii/bwa-samtools-picard
-  ShellCommandRequirement: {}
-  ResourceRequirement:
-    ramMin: 26000
-    coresMin: 16 
-
-hints:
-  arv:RuntimeConstraints:
-    outputDirType: keep_output_dir
-
-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"
-
-arguments:
-  - /bwa-0.7.17/bwa
-  - mem
-  - -M
-  - -t
-  - $(runtime.cores)
-  - $(inputs.reference)
-  - -R
-  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
-  - -c
-  - '250'
-  - $(inputs.fastq1)
-  - $(inputs.fastq2)
-  - shellQuote: false
-    valueFrom: '|'
-  - samtools
-  - view
-  - -@
-  - $(runtime.cores)
-  - -b
-  - -S
-  - shellQuote: false
-    valueFrom: '-'