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authorPjotr Prins2020-05-14 19:01:40 -0500
committerPjotr Prins2020-05-14 19:01:40 -0500
commit5a880b8a4ac1c99e7a6e545b90486e61ae338e9d (patch)
treed086d2167c9894de45d9a42f941c10ed5c016369
parent3ff39327fd531444817a2ce54c37c0bd59752226 (diff)
parent9f901a09a6f5ac95d6875c9e0b435ea9b62fc0f9 (diff)
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Merge branch 'master' of github.com:arvados/bh20-seq-resource
-rw-r--r--bh20simplewebuploader/main.py2
-rw-r--r--workflows/pangenome-generate/pangenome-generate.cwl7
m---------workflows/tools0
3 files changed, 5 insertions, 4 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 2aebe80..e80713f 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -259,7 +259,7 @@ def parse_input(input_string, html_type, number_step=None):
Raise NotImplementedError if we forgot to implement a type.
"""
- if html_type == 'text':
+ if html_type == 'text' or html_type == 'select':
return input_string
elif html_type == 'number':
# May be an int or a float.
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