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| author | Peter Amstutz | 2020-08-19 15:19:07 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | b3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch) | |
| tree | 92adcacbd208546bf3f063e6c25765e660972244 /workflows/pangenome-generate/arv-main.cwl | |
| parent | 592c921a3223c03d8a22f7a852641ac5d753fb31 (diff) | |
| download | bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.gz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.lz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.zip | |
Consolidate steps to scale graph generation workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/arv-main.cwl')
| -rw-r--r-- | workflows/pangenome-generate/arv-main.cwl | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/arv-main.cwl b/workflows/pangenome-generate/arv-main.cwl new file mode 100644 index 0000000..176cfe7 --- /dev/null +++ b/workflows/pangenome-generate/arv-main.cwl @@ -0,0 +1,48 @@ +cwlVersion: v1.1 +class: Workflow +requirements: + SubworkflowFeatureRequirement: {} +inputs: + src_project: string + metadataSchema: File + exclude: File? +outputs: + odgiGraph: + type: File + outputSource: pangenome-generate/odgiGraph + odgiPNG: + type: File + outputSource: pangenome-generate/odgiPNG + spoaGFA: + type: File + outputSource: pangenome-generate/spoaGFA + odgiRDF: + type: File + outputSource: pangenome-generate/odgiRDF + readsMergeDedup: + type: File + outputSource: pangenome-generate/readsMergeDedup + mergedMetadata: + type: File + outputSource: pangenome-generate/mergedMetadata + indexed_paths: + type: File + outputSource: pangenome-generate/indexed_paths + colinear_components: + type: Directory + outputSource: pangenome-generate/colinear_components +steps: + collect-seqs: + run: collect-seqs.cwl + in: + src_project: src_project + schema: metadataSchema + exclude: exclude + out: [relabeledSeqs, mergedMetadata] + pangenome-generate: + run: pangenome-generate_spoa.cwl + in: + seqs: collect-seqs/relabeledSeqs + metadata: collect-seqs/mergedMetadata + exclude: exclude + out: [odgiGraph, odgiPNG, spoaGFA, odgiRDF, readsMergeDedup, mergedMetadata, indexed_paths, colinear_components] |