Merge pull request #112 from icgc-argo/payload-add-uniform-ids@0.1.1

[release]

Author: junjun-zhang

payload-add-uniform-ids/main.nf

@@ -24,7 +24,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-add-uniform-ids'

payload-add-uniform-ids/main.py

@@ -36,17 +36,17 @@ def get_id_mapping(id_mapping_tsv):
             submitter_id = row['submitter_id']
             uniform_id = row['uniform_id']
             if type in id_mapping:
-                sys.exit(f"Values in 'type' field duplicated. Offending value: {type}, in file: {args.id_mapping_tsv}")
+                sys.exit(f"Values in 'type' field duplicated. Offending value: {type}, in file: {id_mapping_tsv}")
             else:
                 id_mapping[type] = dict()
 
             if submitter_id in id_mapping[type]:
-                sys.exit(f"Values in 'submitter_id' field duplicated. Offending value: {submitter_id}, for type: {type}, in file: {args.id_mapping_tsv}" )
+                sys.exit(f"Values in 'submitter_id' field duplicated. Offending value: {submitter_id}, for type: {type}, in file: {id_mapping_tsv}" )
             else:
                 id_mapping[type][submitter_id] = uniform_id
 
     if 'donor' not in id_mapping or 'specimen' not in id_mapping or 'sample' not in id_mapping:
-        sys.exit(f"Provided id_mapping_tsv file '{args.id_mapping_tsv}' is required to have ID mappings for 'donor', 'specimen' and 'sample'")
+        sys.exit(f"Provided id_mapping_tsv file '{id_mapping_tsv}' is required to have ID mappings for 'donor', 'specimen' and 'sample'")
 
     return id_mapping
 

payload-add-uniform-ids/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "payload-add-uniform-ids",
-    "version": "0.1.0",
+    "version": "0.1.1",
     "description": "SONG payload utility tool for adding uniform IDs",
     "main": "main.nf",
     "deprecated": false,