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| author | Peter Amstutz | 2020-11-18 17:03:01 -0500 |
|---|---|---|
| committer | Peter Amstutz | 2020-11-18 17:05:12 -0500 |
| commit | 81daa0acc4c4a0827e1c1198f054f4d4dacd1daf (patch) | |
| tree | b1370c876394e36cb65947dbb37b094536d117ed /workflows/pangenome-generate/pangenome-generate_spoa.cwl | |
| parent | ee8ea88dd6b372143c6b08f56856666ce2d0b622 (diff) | |
| download | bh20-seq-resource-81daa0acc4c4a0827e1c1198f054f4d4dacd1daf.tar.gz bh20-seq-resource-81daa0acc4c4a0827e1c1198f054f4d4dacd1daf.tar.lz bh20-seq-resource-81daa0acc4c4a0827e1c1198f054f4d4dacd1daf.zip | |
Add query-to-gfa workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate_spoa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate_spoa.cwl | 54 |
1 files changed, 27 insertions, 27 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl index fdf3d9f..a640d15 100644 --- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl +++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl @@ -19,15 +19,15 @@ outputs: odgiGraph: type: File outputSource: buildGraph/odgiGraph -# odgiPNG: -# type: File -# outputSource: vizGraph/graph_image + odgiPNG: + type: File + outputSource: vizGraph/graph_image spoaGFA: type: File outputSource: induceGraph/spoaGFA - odgiRDF: - type: File - outputSource: odgi2rdf/rdf +# odgiRDF: +# type: File +# outputSource: odgi2rdf/rdf readsMergeDedupSortedByQualAndLen: type: File outputSource: dedup_and_sort_by_quality_and_len/sortedReadsFA @@ -54,27 +54,27 @@ steps: in: {inputGFA: induceGraph/spoaGFA} out: [odgiGraph] run: odgi-build-from-spoa-gfa.cwl - # vizGraph: - # in: - # sparse_graph_index: buildGraph/odgiGraph - # width: - # default: 50000 - # height: - # default: 500 - # path_per_row: - # default: true - # path_height: - # default: 4 - # out: [graph_image] - # requirements: - # ResourceRequirement: - # ramMin: $(15 * 1024) - # outdirMin: 10 - # run: ../tools/odgi/odgi_viz.cwl - odgi2rdf: - in: {odgi: buildGraph/odgiGraph} - out: [rdf] - run: odgi_to_rdf.cwl + vizGraph: + in: + sparse_graph_index: buildGraph/odgiGraph + width: + default: 50000 + height: + default: 500 + path_per_row: + default: true + path_height: + default: 4 + out: [graph_image] + requirements: + ResourceRequirement: + ramMin: $(15 * 1024) + outdirMin: 10 + run: ../tools/odgi/odgi_viz.cwl + # odgi2rdf: + # in: {odgi: buildGraph/odgiGraph} + # out: [rdf] + # run: odgi_to_rdf.cwl dups2metadata: in: metadata: metadata |