From b3d2ccf951903ac0b7d717357fb1cccca26fbd15 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Wed, 19 Aug 2020 15:19:07 -0400
Subject: Consolidate steps to scale graph generation workflow

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 workflows/pangenome-generate/spoa.cwl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

diff --git a/workflows/pangenome-generate/spoa.cwl b/workflows/pangenome-generate/spoa.cwl
index 1e390d8..132633c 100644
--- a/workflows/pangenome-generate/spoa.cwl
+++ b/workflows/pangenome-generate/spoa.cwl
@@ -2,8 +2,7 @@ cwlVersion: v1.1
 class: CommandLineTool
 inputs:
   readsFA: File
-stdout: $(inputs.readsFA.nameroot).g6.gfa
-script:
+  script:
     type: File
     default: {class: File, location: relabel-seqs.py}
 outputs:
@@ -20,6 +19,7 @@ hints:
     ramMin: $(15 * 1024)
     outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
 baseCommand: spoa
+stdout: $(inputs.readsFA.nameroot).g6.gfa
 arguments: [
     $(inputs.readsFA),
     -G,
-- 
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