Improving genbank import workflow

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
--- /dev/null
+++ 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