diff options
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] |