From 6599feb6a6f8b488bd2d12fcf532c3b8a917a17f Mon Sep 17 00:00:00 2001
From: Michael R. Crusoe
Date: Tue, 5 May 2020 13:11:02 +0200
Subject: move some tools into the shared repo

---
 workflows/pangenome-generate/seqkit-rmdup.cwl | 37 ---------------------------
 1 file changed, 37 deletions(-)
 delete mode 100644 workflows/pangenome-generate/seqkit-rmdup.cwl

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

diff --git a/workflows/pangenome-generate/seqkit-rmdup.cwl b/workflows/pangenome-generate/seqkit-rmdup.cwl
deleted file mode 100644
index 071fa66..0000000
--- a/workflows/pangenome-generate/seqkit-rmdup.cwl
+++ /dev/null
@@ -1,37 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-inputs:
-  readsFA: File
-outputs:
-  readsMergeDedup:
-    type: File
-    outputBinding:
-      glob: readsMergeDedup.fasta
-  dups:
-    type: File?
-    outputBinding:
-      glob: dups.txt
-requirements:
-  InlineJavascriptRequirement: {}
-hints:
-  DockerRequirement:
-    dockerPull: "quay.io/biocontainers/seqkit:0.7.1--0"
-  ResourceRequirement:
-    coresMin: 8
-    coresMax: 32
-    ramMin: $(7 * 1024)
-    outdirMin: |
-      ${
-        var sum = 0;
-        for (var i = 0; i < inputs.readsFA.length; i++) {
-          sum += inputs.readsFA[i].size;
-        }
-        return (sum/(1024*1024*1024)+1) + 20;
-      }
-baseCommand: seqkit
-arguments: [rmdup,
-            --by-seq,
-            --ignore-case,
-            --dup-num-file, dups.txt,
-            -o, readsMergeDedup.fasta,
-            $(inputs.readsFA)]
-- 
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