Merge branch 'blog-examples'

[arvados-tutorial.git] / blog-examples / debugging / star-index / STAR-index.cwl

diff --git a/blog-examples/debugging/star-index/STAR-index.cwl b/blog-examples/debugging/star-index/STAR-index.cwl
new file mode 100755 (executable)
index 0000000..74ee7db
--- /dev/null
+++ b/blog-examples/debugging/star-index/STAR-index.cwl
@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
+  ResourceRequirement:
+    coresMin: 2
+    ramMin: 12000
+
+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)/