aboutsummaryrefslogtreecommitdiff
path: root/workflows/pangenome-generate
diff options
context:
space:
mode:
authorPjotr Prins2020-05-15 09:04:28 -0500
committerPjotr Prins2020-05-15 09:04:28 -0500
commit51503d89df4f5568f503f80c5cbc4fc3325c70aa (patch)
treebbc539c5d7eabfd243c6f6269c56c55360bd650f /workflows/pangenome-generate
parent2c5d48abae99f1114ce4b4f3ed7e81b594394886 (diff)
parent79a85f846671d575eae6f83d96659c0e1be06011 (diff)
downloadbh20-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.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 ]