X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/35d7db9545d96c6f154aabf6c78a66e4dcede3b6..d2f6d47da38e96de4597bb58ba1193e261af8fb1:/make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl

diff --git a/make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl b/make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl
new file mode 100644
index 0000000..9ef1133
--- /dev/null
+++ b/make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl
@@ -0,0 +1,54 @@
+$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]