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| author | Peter Amstutz | 2020-08-19 15:14:45 -0400 |
|---|---|---|
| committer | GitHub | 2020-08-19 15:14:45 -0400 |
| commit | 795d022f4a876ae1cd7df54173fa3927969afe8d (patch) | |
| tree | 734d620bc7ad8803cc459e605fcdb19b52830227 /workflows/pangenome-generate/pangenome-generate_spoa.cwl | |
| parent | fdb1b012fc04ee07f401541e181e28fe442c9454 (diff) | |
| parent | 0cee8cc13b869ef389c941f662c3cef2409e1e61 (diff) | |
| download | bh20-seq-resource-795d022f4a876ae1cd7df54173fa3927969afe8d.tar.gz bh20-seq-resource-795d022f4a876ae1cd7df54173fa3927969afe8d.tar.lz bh20-seq-resource-795d022f4a876ae1cd7df54173fa3927969afe8d.zip | |
Merge pull request #100 from AndreaGuarracino/patch-3
integrated the deduplication step in the sorting by quality and length script
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate_spoa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate_spoa.cwl | 16 |
1 files changed, 6 insertions, 10 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl index 958ffb6..8b34ff8 100644 --- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl +++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl @@ -31,9 +31,9 @@ outputs: odgiRDF: type: File outputSource: odgi2rdf/rdf - readsMergeDedup: + readsMergeDedupSortedByQualAndLen: type: File - outputSource: dedup/reads_dedup + outputSource: dedup_and_sort_by_quality_and_len/reads_dedupped_sorted_by_quality_and_len mergedMetadata: type: File outputSource: mergeMetadata/merged @@ -51,17 +51,13 @@ steps: exclude: exclude out: [relabeledSeqs, originalLabels] run: relabel-seqs.cwl - dedup: + dedup_and_sort_by_quality_and_len: in: {reads: relabel/relabeledSeqs} - out: [reads_dedup, dups] - run: ../tools/seqkit/seqkit_rmdup.cwl - sort_by_quality_and_len: - in: {reads: dedup/reads_dedup} - out: [reads_sorted_by_quality_and_len] + out: [reads_dedupped_sorted_by_quality_and_len, dups] run: sort_fasta_by_quality_and_len.cwl induceGraph: in: - readsFA: sort_by_quality_and_len/reads_sorted_by_quality_and_len + readsFA: dedup_and_sort_by_quality_and_len/reads_dedupped_sorted_by_quality_and_len out: [spoaGFA] run: spoa.cwl buildGraph: @@ -90,7 +86,7 @@ steps: metadata: metadata metadataSchema: metadataSchema subjects: subjects - dups: dedup/dups + dups: dedup_and_sort_by_quality_and_len/dups originalLabels: relabel/originalLabels out: [merged] run: merge-metadata.cwl |