From 618f956eb03c6a6ad1cc16efc931f55b0dce83e1 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Mon, 27 Jul 2020 17:27:07 +0200
Subject: added workflow to sort a multifasta by quality and length, and added
 the overall new pangenome generation workflow with SPOA

---
 .../sort_fasta_by_quality_and_len.cwl                  | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl

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

diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
new file mode 100644
index 0000000..59f027e
--- /dev/null
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -0,0 +1,18 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA:
+    type: File
+    inputBinding: {position: 2}
+  script:
+    type: File
+    inputBinding: {position: 1}
+    default: {class: File, location: sort_fasta_by_quality_and_len.py}
+stdout: $(inputs.readsFA.nameroot).sorted_by_quality_and_len.fasta
+outputs:
+  sortedReadsFA:
+    type: stdout
+requirements:
+  InlineJavascriptRequirement: {}
+  ShellCommandRequirement: {}
+baseCommand: [python]
-- 
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