Add workflow to generate single chromosome fastqs

[arvados-tutorial.git] / make-singlechromfastq / bam2singlechromfastq.cwl

diff --git a/make-singlechromfastq/bam2singlechromfastq.cwl b/make-singlechromfastq/bam2singlechromfastq.cwl
new file mode 100644 (file)
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+++ b/make-singlechromfastq/bam2singlechromfastq.cwl
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+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+cwlVersion: v1.1
+class: CommandLineTool
+label: Convert one chromosome of bam to fastqs
+requirements:
+  ShellCommandRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: curii/bwa-samtools
+  ResourceRequirement:
+    ramMin: 20000
+    coresMin: 4
+  arv:RuntimeConstraints:
+    keep_cache: 9216
+    outputDirType: keep_output_dir
+  SoftwareRequirement:
+    packages:
+      Samtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+        version: [ "1.10" ]
+inputs:
+  bam:
+    type: File
+    #format: edam:format_2572 # BAM
+    label: Alignments in BAM format
+    secondaryFiles: [.bai]
+  sample:
+    type: string
+    label: Sample name
+  chrom:
+    type: string
+    label: Chromosome name
+outputs:
+  fastq1:
+    type: File
+    #format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R1)
+    outputBinding:
+      glob: "*_1.fastq.gz"
+  fastq2:
+    type: File
+    #format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R2)
+    outputBinding:
+      glob: "*_2.fastq.gz"
+baseCommand: [samtools, view]
+arguments:
+  - "-b"
+  - $(inputs.bam)
+  - $(inputs.chrom)
+  - shellQuote: false
+    valueFrom: "|"
+  - "samtools"
+  - "sort"
+  - "-n"
+  - "-"
+  - shellQuote: false
+    valueFrom: "|"
+  - "samtools"
+  - "fastq"
+  - "-@"
+  - $(runtime.cores)
+  - "-"
+  - "-N"
+  - prefix: "-0"
+    valueFrom: "/dev/null"
+  - prefix: "-s"
+    valueFrom: "/dev/null"
+  - prefix: "-1"
+    valueFrom: $(inputs.sample)_1.fastq.gz
+  - prefix: "-2"
+    valueFrom: $(inputs.sample)_2.fastq.gz