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| author | Peter Amstutz | 2020-04-20 14:57:25 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 14:57:25 -0400 |
| commit | 9ddcfeacb3191638f42b08af999889d867f0f81c (patch) | |
| tree | 4cfe4c2b1df38bf6e5c79f5f8c0700407f76a472 /workflows/pangenome-generate/pangenome-generate.cwl | |
| parent | d29dfd593233541b85c1cefb239650279d57d59f (diff) | |
| download | bh20-seq-resource-9ddcfeacb3191638f42b08af999889d867f0f81c.tar.gz bh20-seq-resource-9ddcfeacb3191638f42b08af999889d867f0f81c.tar.lz bh20-seq-resource-9ddcfeacb3191638f42b08af999889d867f0f81c.zip | |
Better handling of duplicate sequences
Also save original fasta label in metadata
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate.cwl')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate.cwl | 10 |
1 files changed, 4 insertions, 6 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl index 896f936..0cb1368 100644 --- a/workflows/pangenome-generate/pangenome-generate.cwl +++ b/workflows/pangenome-generate/pangenome-generate.cwl @@ -26,15 +26,11 @@ steps: in: readsFA: inputReads subjects: subjects - out: [relabeledSeqs] + out: [relabeledSeqs, originalLabels] run: relabel-seqs.cwl - common: - in: {readsFA: relabel/relabeledSeqs} - out: [duplicatedReads] - run: seqkit-common.cwl dedup: in: {readsFA: relabel/relabeledSeqs} - out: [readsMergeDedup] + out: [readsMergeDedup, dups] run: seqkit-rmdup.cwl overlapReads: in: {readsFA: dedup/readsMergeDedup} @@ -63,5 +59,7 @@ steps: metadata: metadata metadataSchema: metadataSchema subjects: subjects + dups: dedup/dups + originalLabels: relabel/originalLabels out: [merged] run: merge-metadata.cwl |