X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/cac99e0d9185a3817a89a245921bbf25c946434d..5b4f2a85bedfad9e72e406e3e1990afc913c9da2:/RNA-Seq/cwl/helper/featureCounts.cwl

diff --git a/RNA-Seq/cwl/helper/featureCounts.cwl b/RNA-Seq/cwl/helper/featureCounts.cwl
new file mode 100644
index 0000000..a17163f
--- /dev/null
+++ b/RNA-Seq/cwl/helper/featureCounts.cwl
@@ -0,0 +1,25 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+inputs:
+  gtf: File
+  counts_input_bam:
+   - File
+   - File[]
+
+baseCommand: featureCounts
+
+arguments: [-T, $(runtime.cores),
+            -a, $(inputs.gtf),
+            -o, featurecounts.tsv,
+            $(inputs.counts_input_bam)]
+
+outputs:
+  featurecounts:
+    type: File
+    outputBinding:
+      glob: featurecounts.tsv
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/subread:1.5.0p3--0