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author | Peter Amstutz | 2020-05-11 10:38:15 -0400 |
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committer | GitHub | 2020-05-11 10:38:15 -0400 |
commit | 55bab826fda6c6bc3190476f8e2c61e51ef092d6 (patch) | |
tree | 02cc9ec2a79fa0c04ded33ccec009ebe03331f39 /workflows/pangenome-generate/seqkit-rmdup.cwl | |
parent | 20b446c79420b1d5c9742caed6713b7a3e5991f4 (diff) | |
parent | ca7df27a6349e7b7009e1d1d5fec372106a072b1 (diff) | |
download | bh20-seq-resource-55bab826fda6c6bc3190476f8e2c61e51ef092d6.tar.gz bh20-seq-resource-55bab826fda6c6bc3190476f8e2c61e51ef092d6.tar.lz bh20-seq-resource-55bab826fda6c6bc3190476f8e2c61e51ef092d6.zip |
Merge pull request #49 from mr-c/add_pangenome_browser_prep
add pangenome browser prep
Diffstat (limited to 'workflows/pangenome-generate/seqkit-rmdup.cwl')
-rw-r--r-- | workflows/pangenome-generate/seqkit-rmdup.cwl | 37 |
1 files changed, 0 insertions, 37 deletions
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)] |