From 088d0a7fa47d4dff5a38f42fe4d12b9841bb033e Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Thu, 23 Jul 2020 22:28:37 +0200
Subject: new workflow for odgi building from spoa gfa

---
 .../odgi-build-from-spoa-gfa.cwl                   | 29 ++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl

diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl
new file mode 100644
index 0000000..2459ce7
--- /dev/null
+++ b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  inputGFA: File
+outputs:
+  odgiGraph:
+    type: File
+    outputBinding:
+      glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+requirements:
+  InlineJavascriptRequirement: {}
+  ShellCommandRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/odgi:v0.3--py37h8b12597_0"
+  ResourceRequirement:
+    coresMin: 4
+    ramMin: $(7 * 1024)
+    outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2))
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.inputGFA)
+        writable: true
+arguments: [odgi, build, -g, $(inputs.inputGFA), -o, -,
+            {shellQuote: false, valueFrom: "|"},
+            odgi, unchop, -i, -, -o, -,
+            {shellQuote: false, valueFrom: "|"},
+            odgi, sort, -i, -, -p, s, -o, $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+           ]
-- 
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