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| author | LLTommy | 2020-04-23 20:18:36 +0200 |
|---|---|---|
| committer | GitHub | 2020-04-23 20:18:36 +0200 |
| commit | 7049cd5d29acd601ccbbc9d04f001b84a51e9bd5 (patch) | |
| tree | 34a1254d81c2e526427fedb1deaa9f8441e8b260 /workflows/pangenome-generate/pangenome-generate.cwl | |
| parent | f38b9c6f22b82327df9648938a5a4bcf863d8c41 (diff) | |
| parent | c7612e7eda5cd38bfbb2d293bebf732893a41b6c (diff) | |
| download | bh20-seq-resource-7049cd5d29acd601ccbbc9d04f001b84a51e9bd5.tar.gz bh20-seq-resource-7049cd5d29acd601ccbbc9d04f001b84a51e9bd5.tar.lz bh20-seq-resource-7049cd5d29acd601ccbbc9d04f001b84a51e9bd5.zip | |
Merge branch 'master' into patch-3
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate.cwl')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate.cwl | 15 |
1 files changed, 13 insertions, 2 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl index 2710743..6794e2d 100644 --- a/workflows/pangenome-generate/pangenome-generate.cwl +++ b/workflows/pangenome-generate/pangenome-generate.cwl @@ -18,13 +18,22 @@ outputs: odgiRDF: type: File outputSource: odgi2rdf/rdf + readsMergeDedup: + type: File + outputSource: dedup/readsMergeDedup mergedMetadata: type: File outputSource: mergeMetadata/merged steps: + relabel: + in: + readsFA: inputReads + subjects: subjects + out: [relabeledSeqs, originalLabels] + run: relabel-seqs.cwl dedup: - in: {readsFA: inputReads} - out: [readsMergeDedup] + in: {readsFA: relabel/relabeledSeqs} + out: [readsMergeDedup, dups] run: seqkit-rmdup.cwl overlapReads: in: {readsFA: dedup/readsMergeDedup} @@ -53,5 +62,7 @@ steps: metadata: metadata metadataSchema: metadataSchema subjects: subjects + dups: dedup/dups + originalLabels: relabel/originalLabels out: [merged] run: merge-metadata.cwl |