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/arv-main.cwl | 48 +++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 workflows/pangenome-generate/arv-main.cwl

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

diff --git a/workflows/pangenome-generate/arv-main.cwl b/workflows/pangenome-generate/arv-main.cwl
new file mode 100644
index 0000000..176cfe7
--- /dev/null
+++ b/workflows/pangenome-generate/arv-main.cwl
@@ -0,0 +1,48 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  SubworkflowFeatureRequirement: {}
+inputs:
+  src_project: string
+  metadataSchema: File
+  exclude: File?
+outputs:
+  odgiGraph:
+    type: File
+    outputSource: pangenome-generate/odgiGraph
+  odgiPNG:
+    type: File
+    outputSource: pangenome-generate/odgiPNG
+  spoaGFA:
+    type: File
+    outputSource: pangenome-generate/spoaGFA
+  odgiRDF:
+    type: File
+    outputSource: pangenome-generate/odgiRDF
+  readsMergeDedup:
+    type: File
+    outputSource: pangenome-generate/readsMergeDedup
+  mergedMetadata:
+    type: File
+    outputSource: pangenome-generate/mergedMetadata
+  indexed_paths:
+    type: File
+    outputSource: pangenome-generate/indexed_paths
+  colinear_components:
+    type: Directory
+    outputSource: pangenome-generate/colinear_components
+steps:
+  collect-seqs:
+    run: collect-seqs.cwl
+    in:
+      src_project: src_project
+      schema: metadataSchema
+      exclude: exclude
+    out: [relabeledSeqs, mergedMetadata]
+  pangenome-generate:
+    run: pangenome-generate_spoa.cwl
+    in:
+      seqs: collect-seqs/relabeledSeqs
+      metadata: collect-seqs/mergedMetadata
+      exclude: exclude
+    out: [odgiGraph, odgiPNG, spoaGFA, odgiRDF, readsMergeDedup, mergedMetadata, indexed_paths, colinear_components]
-- 
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