From d29dfd593233541b85c1cefb239650279d57d59f Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 13:41:56 -0400
Subject: Relabel sequences to match metadata subjects.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 workflows/pangenome-generate/relabel-seqs.cwl | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 workflows/pangenome-generate/relabel-seqs.cwl

(limited to 'workflows/pangenome-generate/relabel-seqs.cwl')

diff --git a/workflows/pangenome-generate/relabel-seqs.cwl b/workflows/pangenome-generate/relabel-seqs.cwl
new file mode 100644
index 0000000..b5b7231
--- /dev/null
+++ b/workflows/pangenome-generate/relabel-seqs.cwl
@@ -0,0 +1,19 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File[]
+  subjects: string[]
+outputs:
+  relabeledSeqs:
+    type: stdout
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entry: {$include: relabel-seqs.py}
+        entryname: relabel-seqs.py
+hints:
+  DockerRequirement:
+    dockerPull: commonworkflowlanguage/cwltool_module
+stdout: relabeledSeqs.fasta
+baseCommand: [python, relabel-seqs.py]
-- 
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