diff options
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate.cwl')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate.cwl | 12 |
1 files changed, 11 insertions, 1 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl index 2710743..896f936 100644 --- a/workflows/pangenome-generate/pangenome-generate.cwl +++ b/workflows/pangenome-generate/pangenome-generate.cwl @@ -22,8 +22,18 @@ outputs: type: File outputSource: mergeMetadata/merged steps: + relabel: + in: + readsFA: inputReads + subjects: subjects + out: [relabeledSeqs] + run: relabel-seqs.cwl + common: + in: {readsFA: relabel/relabeledSeqs} + out: [duplicatedReads] + run: seqkit-common.cwl dedup: - in: {readsFA: inputReads} + in: {readsFA: relabel/relabeledSeqs} out: [readsMergeDedup] run: seqkit-rmdup.cwl overlapReads: |