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| author | AndreaGuarracino | 2020-11-21 22:00:34 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2020-11-21 22:00:34 +0100 |
| commit | 862ae0235e3d1b105fa342cedf4aa59ae73d90c4 (patch) | |
| tree | 618e659d639782b570ba4b16c61a4977f2da6cfa | |
| parent | 3c35250eb6394ec8d0e28e4391ec23f2223345c8 (diff) | |
| download | bh20-seq-resource-862ae0235e3d1b105fa342cedf4aa59ae73d90c4.tar.gz bh20-seq-resource-862ae0235e3d1b105fa342cedf4aa59ae73d90c4.tar.lz bh20-seq-resource-862ae0235e3d1b105fa342cedf4aa59ae73d90c4.zip | |
added reversed_sorting parameter; typos
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate_spoa.cwl | 5 | ||||
| -rw-r--r-- | workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl | 5 |
2 files changed, 8 insertions, 2 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl index a46524a..4e7302d 100644 --- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl +++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl @@ -15,6 +15,9 @@ inputs: type: int default: 100 doc: Cells per file on component_segmentation + reversed_sort: + type: string + default: "true" outputs: odgiGraph: type: File @@ -42,7 +45,7 @@ outputs: # outputSource: segment_components/colinear_components steps: dedup_and_sort_by_quality_and_len: - in: {readsFA: seqs, reversed_sorting: 'true'} + in: {readsFA: seqs, reversed_sorting: reversed_sort} out: [sortedReadsFA, dups] run: sort_fasta_by_quality_and_len.cwl induceGraph: diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl index f8df786..6f71d92 100644 --- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl +++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl @@ -1,3 +1,4 @@ + cwlVersion: v1.1 class: CommandLineTool hints: @@ -5,7 +6,8 @@ hints: coresMin: 1 ramMin: 3000 inputs: - reversed_sorting: + reversed_sorting: + type: string inputBinding: {position: 3} readsFA: type: File @@ -25,3 +27,4 @@ requirements: InlineJavascriptRequirement: {} ShellCommandRequirement: {} baseCommand: [python] + |