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| author | Pjotr Prins | 2020-05-15 09:04:28 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-05-15 09:04:28 -0500 |
| commit | 51503d89df4f5568f503f80c5cbc4fc3325c70aa (patch) | |
| tree | bbc539c5d7eabfd243c6f6269c56c55360bd650f /workflows/pangenome-generate | |
| parent | 2c5d48abae99f1114ce4b4f3ed7e81b594394886 (diff) | |
| parent | 79a85f846671d575eae6f83d96659c0e1be06011 (diff) | |
| download | bh20-seq-resource-51503d89df4f5568f503f80c5cbc4fc3325c70aa.tar.gz bh20-seq-resource-51503d89df4f5568f503f80c5cbc4fc3325c70aa.tar.lz bh20-seq-resource-51503d89df4f5568f503f80c5cbc4fc3325c70aa.zip | |
Merge branch 'master' of github.com:arvados/bh20-seq-resource
Diffstat (limited to 'workflows/pangenome-generate')
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate.cwl | 7 |
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 ] |