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| author | Peter Amstutz | 2020-08-19 16:31:26 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | 25bab899cbe8871cbb9530fc768a1cd7ab4daba1 (patch) | |
| tree | 638e8e0b9dd7be0aa01ab5490199f621bdfcb6af /workflows/pangenome-generate | |
| parent | d1e8809a15ae74d0b847abb80f9f63f53078e1d6 (diff) | |
| download | bh20-seq-resource-25bab899cbe8871cbb9530fc768a1cd7ab4daba1.tar.gz bh20-seq-resource-25bab899cbe8871cbb9530fc768a1cd7ab4daba1.tar.lz bh20-seq-resource-25bab899cbe8871cbb9530fc768a1cd7ab4daba1.zip | |
Fix output parameters
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate')
| -rw-r--r-- | workflows/pangenome-generate/arv-main.cwl | 4 | ||||
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate_spoa.cwl | 6 |
2 files changed, 5 insertions, 5 deletions
diff --git a/workflows/pangenome-generate/arv-main.cwl b/workflows/pangenome-generate/arv-main.cwl index 8d7f83b..dae47e6 100644 --- a/workflows/pangenome-generate/arv-main.cwl +++ b/workflows/pangenome-generate/arv-main.cwl @@ -21,7 +21,7 @@ outputs: outputSource: pangenome-generate/odgiRDF readsMergeDedup: type: File - outputSource: pangenome-generate/readsMergeDedup + outputSource: pangenome-generate/readsMergeDedupSortedByQualAndLen mergedMetadata: type: File outputSource: pangenome-generate/mergedMetadata @@ -45,4 +45,4 @@ steps: seqs: collect-seqs/relabeledSeqs metadata: collect-seqs/mergedMetadata exclude: exclude - out: [odgiGraph, spoaGFA, odgiRDF, readsMergeDedup, mergedMetadata] + out: [odgiGraph, spoaGFA, odgiRDF, readsMergeDedupSortedByQualAndLen, mergedMetadata] diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl index ed12254..fdf3d9f 100644 --- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl +++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl @@ -30,7 +30,7 @@ outputs: outputSource: odgi2rdf/rdf readsMergeDedupSortedByQualAndLen: type: File - outputSource: dedup_and_sort_by_quality_and_len/reads_dedupped_sorted_by_quality_and_len + outputSource: dedup_and_sort_by_quality_and_len/sortedReadsFA mergedMetadata: type: File outputSource: dups2metadata/merged @@ -42,12 +42,12 @@ outputs: # outputSource: segment_components/colinear_components steps: dedup_and_sort_by_quality_and_len: - in: {reads: seqs} + in: {readsFA: seqs} out: [sortedReadsFA, dups] run: sort_fasta_by_quality_and_len.cwl induceGraph: in: - readsFA: dedup_and_sort_by_quality_and_len/reads_dedupped_sorted_by_quality_and_len + readsFA: dedup_and_sort_by_quality_and_len/sortedReadsFA out: [spoaGFA] run: spoa.cwl buildGraph: |