Adding RNA-Seq demo

[arvados-tutorial.git] / RNA-Seq / cwl / helper / alignment.cwl

diff --git a/RNA-Seq/cwl/helper/alignment.cwl b/RNA-Seq/cwl/helper/alignment.cwl
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+++ b/RNA-Seq/cwl/helper/alignment.cwl
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+cwlVersion: v1.2
+class: Workflow
+label: RNAseq CWL practice workflow
+
+inputs:
+  fq: File
+  genome: Directory
+  gtf: File
+
+requirements:
+  StepInputExpressionRequirement: {}
+
+steps:
+  fastqc:
+    run: bio-cwl-tools/fastqc/fastqc_2.cwl
+    in:
+      reads_file: fq
+    out: [html_file]
+
+  STAR:
+    requirements:
+      ResourceRequirement:
+        ramMin: 9000
+    run: bio-cwl-tools/STAR/STAR-Align.cwl
+    in:
+      RunThreadN: {default: 4}
+      GenomeDir: genome
+      ForwardReads: fq
+      OutSAMtype: {default: BAM}
+      SortedByCoordinate: {default: true}
+      OutSAMunmapped: {default: Within}
+      ### 1. Expressions on step inputs
+      OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
+    out: [alignment]
+
+  samtools:
+    run: bio-cwl-tools/samtools/samtools_index.cwl
+    in:
+      bam_sorted: STAR/alignment
+    out: [bam_sorted_indexed]
+
+outputs:
+  qc_html:
+    type: File
+    outputSource: fastqc/html_file
+  bam_sorted_indexed:
+    type: File
+    outputSource: samtools/bam_sorted_indexed