Add workflow to generate single chromosome fastqs

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

diff --git a/make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl b/make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl
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+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+cwlVersion: v1.1
+class: Workflow
+label: Scatter to convert one chromosome of bam to fastqs
+requirements:
+  ScatterFeatureRequirement: {}
+
+inputs:
+  bams:
+    type:
+      type: array
+      items: File
+    format: edam:format_2572 # BAM
+    secondaryFiles: [.bai]
+    label: Alignments in BAM format
+  samples:
+    type:
+      type: array
+      items: string
+    label: Sample names
+  chrom:
+    type: string
+    label: Chromosome name
+
+outputs:
+  fastq1s:
+    type:
+      type: array
+      items: File
+    format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R1)
+    outputSource: bam2singlechromfastq/fastq1
+  fastq2s:
+    type:
+      type: array
+      items: File
+    format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R2)
+    outputSource: bam2singlechromfastq/fastq2
+
+steps:
+  bam2singlechromfastq:
+    run: bam2singlechromfastq.cwl
+    scatter: [bam, sample]
+    scatterMethod: dotproduct
+    in:
+      bam: bams
+      sample: samples
+      chrom: chrom
+    out: [fastq1, fastq2]