aboutsummaryrefslogtreecommitdiff
path: root/workflows/pangenome-generate/pangenome-generate_spoa.cwl
diff options
context:
space:
mode:
authorPeter Amstutz2020-08-19 16:31:26 -0400
committerPeter Amstutz2020-08-19 16:31:38 -0400
commit25bab899cbe8871cbb9530fc768a1cd7ab4daba1 (patch)
tree638e8e0b9dd7be0aa01ab5490199f621bdfcb6af /workflows/pangenome-generate/pangenome-generate_spoa.cwl
parentd1e8809a15ae74d0b847abb80f9f63f53078e1d6 (diff)
downloadbh20-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/pangenome-generate_spoa.cwl')
-rw-r--r--workflows/pangenome-generate/pangenome-generate_spoa.cwl6
1 files changed, 3 insertions, 3 deletions
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: