From 9ddcfeacb3191638f42b08af999889d867f0f81c Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 14:57:25 -0400
Subject: Better handling of duplicate sequences

Also save original fasta label in metadata
---
 workflows/pangenome-generate/relabel-seqs.cwl | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

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

diff --git a/workflows/pangenome-generate/relabel-seqs.cwl b/workflows/pangenome-generate/relabel-seqs.cwl
index b5b7231..2b780d4 100644
--- a/workflows/pangenome-generate/relabel-seqs.cwl
+++ b/workflows/pangenome-generate/relabel-seqs.cwl
@@ -5,7 +5,13 @@ inputs:
   subjects: string[]
 outputs:
   relabeledSeqs:
-    type: stdout
+    type: File
+    outputBinding:
+      glob: relabeledSeqs.fasta
+  originalLabels:
+    type: File
+    outputBinding:
+      glob: originalLabels.ttl
 requirements:
   InlineJavascriptRequirement: {}
   InitialWorkDirRequirement:
@@ -15,5 +21,5 @@ requirements:
 hints:
   DockerRequirement:
     dockerPull: commonworkflowlanguage/cwltool_module
-stdout: relabeledSeqs.fasta
+stdout:
 baseCommand: [python, relabel-seqs.py]
-- 
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