aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--bh20seqanalyzer/main.py2
-rw-r--r--bh20simplewebuploader/main.py2
-rw-r--r--workflows/pangenome-generate/pangenome-generate.cwl7
m---------workflows/tools0
4 files changed, 6 insertions, 5 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 07e5f69..28b5e31 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -146,7 +146,7 @@ def start_pangenome_analysis(api,
"class": "File",
"location": "keep:%s/metadata.yaml" % v["portable_data_hash"]
})
- inputobj["subjects"].append("http://arvados.org/keep:%s/sequence.fasta" % v["portable_data_hash"])
+ inputobj["subjects"].append("http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % v["portable_data_hash"])
run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj)
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