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authorPeter Amstutz2020-08-19 15:14:45 -0400
committerGitHub2020-08-19 15:14:45 -0400
commit795d022f4a876ae1cd7df54173fa3927969afe8d (patch)
tree734d620bc7ad8803cc459e605fcdb19b52830227 /workflows/pangenome-generate/pangenome-generate_spoa.cwl
parentfdb1b012fc04ee07f401541e181e28fe442c9454 (diff)
parent0cee8cc13b869ef389c941f662c3cef2409e1e61 (diff)
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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.cwl16
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