diff options
| author | Pjotr Prins | 2020-12-24 09:15:39 +0000 |
|---|---|---|
| committer | GitHub | 2020-12-24 09:15:39 +0000 |
| commit | df0421757e464f07b5e96b5444f1926784e7400f (patch) | |
| tree | f9a9a262bb2d95a89a6ec1c96b98a2b166fb92b5 /workflows/pangenome-generate/pangenome-generate_spoa.cwl | |
| parent | 00ba74b163f723bb7283624171f0c7c203dc99e5 (diff) | |
| parent | bfd830f9d777c456409958030142155043ec1c68 (diff) | |
| download | bh20-seq-resource-df0421757e464f07b5e96b5444f1926784e7400f.tar.gz bh20-seq-resource-df0421757e464f07b5e96b5444f1926784e7400f.tar.lz bh20-seq-resource-df0421757e464f07b5e96b5444f1926784e7400f.zip | |
Merge pull request #117 from arvados/pangenome_workflow_abpoa
Pangenome workflow with abPOA
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate_spoa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate_spoa.cwl | 7 |
1 files changed, 5 insertions, 2 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl index b623054..fa16809 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} + in: {readsFA: seqs, reversed_sorting: reversed_sort} out: [sortedReadsFA, dups] run: sort_fasta_by_quality_and_len.cwl induceGraph: @@ -53,7 +56,7 @@ steps: buildGraph: in: {inputGFA: induceGraph/spoaGFA} out: [odgiGraph] - run: odgi-build-from-spoa-gfa.cwl + run: odgi-build-from-xpoa-gfa.cwl vizGraph: in: sparse_graph_index: buildGraph/odgiGraph |