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-rw-r--r--scripts/import.cwl8
-rw-r--r--scripts/import_to_arvados.py1
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")