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Diffstat (limited to 'workflows/pangenome-generate/query-to-gfa.cwl')
-rw-r--r-- | workflows/pangenome-generate/query-to-gfa.cwl | 32 |
1 files changed, 32 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/query-to-gfa.cwl b/workflows/pangenome-generate/query-to-gfa.cwl new file mode 100644 index 0000000..2f3a20a --- /dev/null +++ b/workflows/pangenome-generate/query-to-gfa.cwl @@ -0,0 +1,32 @@ +cwlVersion: v1.1 +class: Workflow +requirements: + SubworkflowFeatureRequirement: {} +inputs: + metadata: File + fasta: + type: File + secondaryFiles: [.fai] + query: string +outputs: + odgiGraph: + type: File + outputSource: make-gfa/odgiGraph + spoaGFA: + type: File + outputSource: make-gfa/spoaGFA + readsMergeDedupSortedByQualAndLen: + type: File + outputSource: make-gfa/readsMergeDedupSortedByQualAndLen + mergedMetadata: + type: File + outputSource: make-gfa/mergedMetadata +steps: + get-subset: + run: from_sparql.cwl + in: {metadata: metadata, query: query, fasta: fasta} + out: [selected] + make-gfa: + run: pangenome-generate_spoa.cwl + in: {metadata: metadata, seqs: get-subset/selected} + out: [odgiGraph, spoaGFA, readsMergeDedupSortedByQualAndLen, mergedMetadata] |