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: