From 81daa0acc4c4a0827e1c1198f054f4d4dacd1daf Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Wed, 18 Nov 2020 17:03:01 -0500
Subject: Add query-to-gfa workflow

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 workflows/pangenome-generate/collect-seqs.cwl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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

diff --git a/workflows/pangenome-generate/collect-seqs.cwl b/workflows/pangenome-generate/collect-seqs.cwl
index 635108f..268a08c 100644
--- a/workflows/pangenome-generate/collect-seqs.cwl
+++ b/workflows/pangenome-generate/collect-seqs.cwl
@@ -8,7 +8,7 @@ requirements:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
   DockerRequirement:
-    dockerPull: arvados/jobs:2.0.3
+    dockerImageId: arvados-and-samtools
   WorkReuse:
     enableReuse: false
   ResourceRequirement:
@@ -36,6 +36,7 @@ outputs:
     type: File
     outputBinding:
       glob: relabeledSeqs.fasta
+    secondaryFiles: [.fai]
   mergedMetadata:
     type: File
     outputBinding:
-- 
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