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authorPeter Amstutz2020-05-14 16:47:08 -0400
committerPeter Amstutz2020-05-14 16:47:08 -0400
commita259ff7f26458c0810741508df39a4b391ff18d4 (patch)
tree4620edd4cf336f93f55adea87c71eff43babfa80
parentc44a03772f1fe12bb9a6fe27e242337d14356ff7 (diff)
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Workflow fixes
-rw-r--r--workflows/pangenome-generate/pangenome-generate.cwl7
m---------workflows/tools0
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