Merge pull request #150 from icgc-argo-workflows/payload-gen-rna-alignment@0.1.3

[release]

Author: lindaxiang

payload-gen-rna-alignment/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 = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-rna-alignment'

payload-gen-rna-alignment/main.py

@@ -211,7 +211,7 @@ def get_files_info(file_to_upload, date_str, seq_experiment_analysis_dict, align
     }
 
     if not aligner:
-      file_info['info']['analysis_tools'] = "FastQC"
+      file_info['info']['analysis_tools'] = ["FastQC"]
     elif aligner.lower() == 'star':
       file_info['info']['analysis_tools'] = data_type_mapping[file_type][3]
     elif aligner.lower() == 'hisat2':

payload-gen-rna-alignment/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "payload-gen-rna-alignment",
-    "version": "0.1.2",
+    "version": "0.1.3",
     "description": "payload-gen-rna-alignment",
     "main": "main.nf",
     "deprecated": false,

payload-gen-rna-alignment/tests/checker.nf

@@ -29,7 +29,7 @@
 /* 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 = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-rna-alignment'

payload-gen-rna-alignment/tests/expected/expected.test-job-3.out.json

@@ -8,8 +8,8 @@
     "workflow_version": "0.1.0",
     "genome_build": "GRCh38_hla_decoy_ebv",
     "genome_annotation": "GENCODE v38",
-    "run_id": "sick_hilbert",
-    "session_id": "575a320a-f228-48d7-a311-b8a314d66e6b",
+    "run_id": "lonely_thompson",
+    "session_id": "6fb88d81-ad07-4c1b-bcfa-51e133e836fe",
     "inputs": [
       {
         "analysis_type": "sequencing_experiment",
@@ -27,7 +27,9 @@
         "data_subtypes": [
           "Read Group Metrics"
         ],
-        "analysis_tools": "FastQC",
+        "analysis_tools": [
+          "FastQC"
+        ],
         "files_in_tgz": [
           "TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane_fastqc.html",
           "TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane_fastqc.zip"
@@ -47,7 +49,7 @@
         },
         "description": "High level sequencing reads QC metrics generated by FastQC."
       },
-      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.S01L1.fastqc.tgz",
+      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20220321.S01L1.fastqc.tgz",
       "fileType": "TGZ",
       "dataType": "Sequencing QC"
     }