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| author | Pjotr Prins | 2020-05-14 19:01:40 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-05-14 19:01:40 -0500 |
| commit | 5a880b8a4ac1c99e7a6e545b90486e61ae338e9d (patch) | |
| tree | d086d2167c9894de45d9a42f941c10ed5c016369 /workflows/pangenome-generate/pangenome-generate.cwl | |
| parent | 3ff39327fd531444817a2ce54c37c0bd59752226 (diff) | |
| parent | 9f901a09a6f5ac95d6875c9e0b435ea9b62fc0f9 (diff) | |
| download | bh20-seq-resource-5a880b8a4ac1c99e7a6e545b90486e61ae338e9d.tar.gz bh20-seq-resource-5a880b8a4ac1c99e7a6e545b90486e61ae338e9d.tar.lz bh20-seq-resource-5a880b8a4ac1c99e7a6e545b90486e61ae338e9d.zip | |
Merge branch 'master' of github.com:arvados/bh20-seq-resource
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate.cwl')
| -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 ] |