diff options
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 |