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| author | Peter Amstutz | 2020-05-14 16:47:08 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-05-14 16:47:08 -0400 |
| commit | a259ff7f26458c0810741508df39a4b391ff18d4 (patch) | |
| tree | 4620edd4cf336f93f55adea87c71eff43babfa80 /workflows/pangenome-generate/pangenome-generate.cwl | |
| parent | c44a03772f1fe12bb9a6fe27e242337d14356ff7 (diff) | |
| download | bh20-seq-resource-a259ff7f26458c0810741508df39a4b391ff18d4.tar.gz bh20-seq-resource-a259ff7f26458c0810741508df39a4b391ff18d4.tar.lz bh20-seq-resource-a259ff7f26458c0810741508df39a4b391ff18d4.zip | |
Workflow fixes
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 ] |