X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/ec904dcdfc5ace2774af00636890f2e6f403839b..4292ebf16822fde6b023ca1828bcae97b6d812ce:/blog-examples/debugging/star-index/STAR-index-broken.cwl

diff --git a/blog-examples/debugging/star-index/STAR-index-broken.cwl b/blog-examples/debugging/star-index/STAR-index-broken.cwl
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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
+
+inputs:
+
+  InputFiles:
+    format: http://edamontology.org/format_1930
+    type: File[]
+    inputBinding:
+      prefix: "--genomeFastaFiles"
+
+  IndexName:
+    type: string
+    inputBinding:
+      prefix: "--genomeDir"
+      valueFrom: ./$(self)
+
+#Optional Inputs
+
+  Gtf:
+    type: File?
+    inputBinding:
+      prefix: "--sjdbGTFfile"
+
+  Overhang:
+    type: int?
+    inputBinding:
+      prefix: "--sjdbOverhang"
+
+  Junctions:
+    type: File?
+    inputBinding:
+      prefix: "--sjdbFileChrStartEnd"
+
+  GenomeSize:
+    type: int?
+    inputBinding:
+      prefix: "--genomeSAindexNbases"
+
+  GenomeBits:
+    type: int?
+    inputBinding:
+      prefix: "--genomeChrBinNbits"
+
+baseCommand: [STAR, --runMode, genomeGenerate]
+
+arguments: [--runThreadN, $(runtime.cores)]
+
+outputs:
+  indexes:
+    type: Directory
+    outputBinding:
+      glob: ./$(inputs.IndexName)/