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| author | AndreaGuarracino | 2020-07-27 17:27:07 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-07-27 17:27:07 +0200 |
| commit | 618f956eb03c6a6ad1cc16efc931f55b0dce83e1 (patch) | |
| tree | 6ae7daaf0978347c999dd1fc7926896baa777e8a /workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl | |
| parent | e31d89f6b4c0d2a99eb6df90b85b4e51cb584817 (diff) | |
| download | bh20-seq-resource-618f956eb03c6a6ad1cc16efc931f55b0dce83e1.tar.gz bh20-seq-resource-618f956eb03c6a6ad1cc16efc931f55b0dce83e1.tar.lz bh20-seq-resource-618f956eb03c6a6ad1cc16efc931f55b0dce83e1.zip | |
added workflow to sort a multifasta by quality and length, and added the overall new pangenome generation workflow with SPOA
Diffstat (limited to 'workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl')
| -rw-r--r-- | workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl | 18 |
1 files changed, 18 insertions, 0 deletions
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] |