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authorPeter Amstutz2020-07-03 20:45:17 +0000
committerPeter Amstutz2020-07-03 20:47:14 +0000
commit535b8017ddd27a9db683f6d29368258b5c48cf5a (patch)
tree521a3e446f0eb9cbdc6e8736a13706c8141f8351 /scripts/fetch_from_genbank.cwl
parent841af02eaa45c1b7395d5f4e4711de3c3661c146 (diff)
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Improving genbank import workflow
Diffstat (limited to 'scripts/fetch_from_genbank.cwl')
-rw-r--r--scripts/fetch_from_genbank.cwl49
1 files changed, 49 insertions, 0 deletions
diff --git a/scripts/fetch_from_genbank.cwl b/scripts/fetch_from_genbank.cwl
new file mode 100644
index 0000000..45c8eec
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+++ b/scripts/fetch_from_genbank.cwl
@@ -0,0 +1,49 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+ importScript:
+ type: File
+ default:
+ class: File
+ location: download_genbank_data/from_genbank_to_fasta_and_yaml.py
+ inputBinding: {position: 1}
+ dict:
+ type: Directory
+ inputBinding:
+ prefix: --dict-ontology
+ position: 2
+ default:
+ class: Directory
+ location: dict_ontology_standardization
+ existing_metadata_from_nuccore:
+ type: Directory?
+ inputBinding:
+ valueFrom: "--skip-request"
+ position: 3
+outputs:
+ fasta_and_yaml:
+ type: Directory
+ outputBinding:
+ glob: fasta_and_yaml
+ metadata_from_nuccore:
+ type: Directory
+ outputBinding:
+ glob: metadata_from_nuccore
+ accessions:
+ type: File?
+ outputBinding:
+ glob: "*.acc"
+ missing_terms:
+ type: File
+ outputBinding:
+ glob: missing_terms.tsv
+requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entry: $(inputs.existing_metadata_from_nuccore)
+ entryname: metadata_from_nuccore
+ DockerRequirement:
+ dockerPull: bh20-seq-uploader/import
+ NetworkAccess:
+ networkAccess: true
+baseCommand: python3