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-rw-r--r--workflows/pangenome-generate/arv-main.cwl4
-rw-r--r--workflows/pangenome-generate/pangenome-generate_spoa.cwl6
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: