diff options
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate.cwl | 7 | ||||
| m--------- | workflows/tools | 0 |
2 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 ] diff --git a/workflows/tools b/workflows/tools -Subproject 659e174d0d42ed6b9afd79d9e6f68e225c526d1 +Subproject 1ecbfefa2c064c9b99765a4fb0f84f84e28d35c |