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authorLLTommy2020-04-23 20:18:36 +0200
committerGitHub2020-04-23 20:18:36 +0200
commit7049cd5d29acd601ccbbc9d04f001b84a51e9bd5 (patch)
tree34a1254d81c2e526427fedb1deaa9f8441e8b260 /workflows/pangenome-generate/seqkit-rmdup.cwl
parentf38b9c6f22b82327df9648938a5a4bcf863d8c41 (diff)
parentc7612e7eda5cd38bfbb2d293bebf732893a41b6c (diff)
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Merge branch 'master' into patch-3
Diffstat (limited to 'workflows/pangenome-generate/seqkit-rmdup.cwl')
-rw-r--r--workflows/pangenome-generate/seqkit-rmdup.cwl7
1 files changed, 6 insertions, 1 deletions
diff --git a/workflows/pangenome-generate/seqkit-rmdup.cwl b/workflows/pangenome-generate/seqkit-rmdup.cwl
index d3626f5..071fa66 100644
--- a/workflows/pangenome-generate/seqkit-rmdup.cwl
+++ b/workflows/pangenome-generate/seqkit-rmdup.cwl
@@ -1,12 +1,16 @@
cwlVersion: v1.1
class: CommandLineTool
inputs:
- readsFA: File[]
+ readsFA: File
outputs:
readsMergeDedup:
type: File
outputBinding:
glob: readsMergeDedup.fasta
+ dups:
+ type: File?
+ outputBinding:
+ glob: dups.txt
requirements:
InlineJavascriptRequirement: {}
hints:
@@ -28,5 +32,6 @@ baseCommand: seqkit
arguments: [rmdup,
--by-seq,
--ignore-case,
+ --dup-num-file, dups.txt,
-o, readsMergeDedup.fasta,
$(inputs.readsFA)]