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/collect-seqs.cwl | 42 +++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 workflows/pangenome-generate/collect-seqs.cwl

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

diff --git a/workflows/pangenome-generate/collect-seqs.cwl b/workflows/pangenome-generate/collect-seqs.cwl
new file mode 100644
index 0000000..3511df1
--- /dev/null
+++ b/workflows/pangenome-generate/collect-seqs.cwl
@@ -0,0 +1,42 @@
+cwlVersion: v1.1
+class: CommandLineTool
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+requirements:
+  arv:APIRequirement: {}
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+  DockerRequirement:
+    dockerPull: arvados/jobs:2.0.3
+  WorkReuse:
+    enableReuse: false
+  ResourceRequirement:
+    coresMin: 1
+    ramMin: 1024
+baseCommand: python3
+inputs:
+  script:
+    type: File
+    default:
+      class: File
+      location: collect-seqs.py
+    inputBinding: {position: 1}
+  src_project:
+    type: string
+    inputBinding: {position: 2}
+  schema:
+    type: File
+    inputBinding: {position: 3}
+  exclude:
+    type: File?
+    inputBinding: {position: 4}
+outputs:
+  relabeledSeqs:
+    type: File
+    outputBinding:
+      glob: relabeledSeqs.fasta
+  mergedMetadata:
+    type: File
+    outputBinding:
+      glob: mergedMetadata.ttl
-- 
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