diff options
| -rw-r--r-- | bh20seqanalyzer/main.py | 2 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 2 | ||||
| -rw-r--r-- | workflows/pangenome-generate/pangenome-generate.cwl | 7 | ||||
| m--------- | workflows/tools | 0 |
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 |