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/pangenome-generate.cwl | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

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

diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 2710743..896f936 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -22,8 +22,18 @@ outputs:
     type: File
     outputSource: mergeMetadata/merged
 steps:
+  relabel:
+    in:
+      readsFA: inputReads
+      subjects: subjects
+    out: [relabeledSeqs]
+    run: relabel-seqs.cwl
+  common:
+    in: {readsFA: relabel/relabeledSeqs}
+    out: [duplicatedReads]
+    run: seqkit-common.cwl
   dedup:
-    in: {readsFA: inputReads}
+    in: {readsFA: relabel/relabeledSeqs}
     out: [readsMergeDedup]
     run: seqkit-rmdup.cwl
   overlapReads:
-- 
cgit v1.2.3