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-rw-r--r--workflows/pangenome-generate/pangenome-generate.cwl7
1 files changed, 4 insertions, 3 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 1d49904..ad8b27f 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -57,8 +57,9 @@ steps:
in:
target: dedup/reads_dedup
query: dedup/reads_dedup
- outputCIGAR:
- default: true
+ outputCIGAR: {default: true}
+ preset: {default: asm20}
+ miniWinSize: {default: 1}
out: [alignments]
run: ../tools/minimap2/minimap2_paf.cwl
induceGraph:
@@ -106,7 +107,7 @@ steps:
out: [ bins, pangenome_sequence ]
index_paths:
label: Create path index
- run : ../tools/odgi/odgi_pathindex.cwl
+ run: ../tools/odgi/odgi_pathindex.cwl
in:
sparse_graph_index: buildGraph/odgiGraph
out: [ indexed_paths ]