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/seqkit-rmdup.cwl | 5 +++++
 1 file changed, 5 insertions(+)

(limited to 'workflows/pangenome-generate/seqkit-rmdup.cwl')

diff --git a/workflows/pangenome-generate/seqkit-rmdup.cwl b/workflows/pangenome-generate/seqkit-rmdup.cwl
index d3626f5..07184c3 100644
--- a/workflows/pangenome-generate/seqkit-rmdup.cwl
+++ b/workflows/pangenome-generate/seqkit-rmdup.cwl
@@ -7,6 +7,10 @@ outputs:
     type: File
     outputBinding:
       glob: readsMergeDedup.fasta
+  dups:
+    type: File
+    outputBinding:
+      glob: dups.txt
 requirements:
   InlineJavascriptRequirement: {}
 hints:
@@ -28,5 +32,6 @@ baseCommand: seqkit
 arguments: [rmdup,
             --by-seq,
             --ignore-case,
+            --dup-num-file, dups.txt,
             -o, readsMergeDedup.fasta,
             $(inputs.readsFA)]
-- 
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