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| author | Peter Amstutz | 2020-04-30 10:46:56 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-30 10:46:56 -0400 |
| commit | 02ecf15cdc04270e06f2be7457bb1b284eeddc56 (patch) | |
| tree | 2e2e1db264ae69855a667cb230aca4ce35910359 | |
| parent | 347b8dce36832c6d3e379d81b3efefcbc88a3117 (diff) | |
| download | bh20-seq-resource-02ecf15cdc04270e06f2be7457bb1b284eeddc56.tar.gz bh20-seq-resource-02ecf15cdc04270e06f2be7457bb1b284eeddc56.tar.lz bh20-seq-resource-02ecf15cdc04270e06f2be7457bb1b284eeddc56.zip | |
Import script fixes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| -rw-r--r-- | scripts/import.cwl | 8 | ||||
| -rw-r--r-- | scripts/import_to_arvados.py | 1 |
2 files changed, 8 insertions, 1 deletions
diff --git a/scripts/import.cwl b/scripts/import.cwl index 81752c8..d84516b 100644 --- a/scripts/import.cwl +++ b/scripts/import.cwl @@ -14,6 +14,12 @@ inputs: class: File location: from_genbank_to_fasta_and_yaml.py inputBinding: {position: 2} + dict: + type: Directory + default: + class: Directory + location: dict_ontology_standardization + inputBinding: {position: 3} outputs: [] requirements: DockerRequirement: @@ -21,4 +27,4 @@ requirements: NetworkAccess: networkAccess: true WorkReuse: - workReuse: false + enableReuse: false diff --git a/scripts/import_to_arvados.py b/scripts/import_to_arvados.py index 07b7d71..78cd13d 100644 --- a/scripts/import_to_arvados.py +++ b/scripts/import_to_arvados.py @@ -4,6 +4,7 @@ import glob import sys os.chdir(os.environ["TMPDIR"]) +os.symlink(sys.argv[2], "dict_ontology_standardization") subprocess.run(sys.argv[1]) os.chdir("fasta_and_yaml") |