From 1e9a735e84a8e89099b1de2ec66c56669caf6cc8 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 21 Nov 2020 23:06:05 +0100
Subject: added abPOA workflow; typos

---
 workflows/pangenome-generate/abpoa.cwl | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 workflows/pangenome-generate/abpoa.cwl

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

diff --git a/workflows/pangenome-generate/abpoa.cwl b/workflows/pangenome-generate/abpoa.cwl
new file mode 100644
index 0000000..fa9f157
--- /dev/null
+++ b/workflows/pangenome-generate/abpoa.cwl
@@ -0,0 +1,26 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File
+  script:
+    type: File
+    default: {class: File, location: relabel-seqs.py}
+outputs:
+  abpoaGFA:
+    type: stdout
+requirements:
+  InlineJavascriptRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/abpoa:1.0.5--hed695b0_0"
+  ResourceRequirement:
+    coresMin: 1
+    ramMin: $(15 * 1024)
+    outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
+baseCommand: abpoa
+stdout: $(inputs.readsFA.nameroot).O0.gfa
+arguments: [
+    $(inputs.readsFA),
+    -r 3,
+    -O, '0'
+]
-- 
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