fixes to address pr comments

Author: lindaxiang

payload-gen-rna-alignment/main.py

@@ -45,7 +45,7 @@
 data_type_mapping = {
   #file_type: [dataCategory, dataType, [data_subtypes], [star analysis_tools], [hisat2 analysis_tools]]
   'genome_aln': ['Sequencing Reads', 'Aligned Reads', ['Genome Alignment'], ['STAR'], ['HiSAT2']],
-  'transcriptome_aln': ['Sequencing Reads', 'Aligned Reads', ['transcriptome Alignment'], ['STAR'], ['HiSAT2']],
+  'transcriptome_aln': ['Sequencing Reads', 'Aligned Reads', ['Transcriptome Alignment'], ['STAR'], ['HiSAT2']],
   'chimeric_aln': ['Sequencing Reads', 'Aligned Reads', ['Chimeric Alignment'], ['STAR'], ['HiSAT2']],
   'splice_junctions': ['Transcriptome Profiling', 'Splice Junctions', [None], ['STAR'], ['HiSAT2']],
   'fastqc': ['Quality Control Metrics', 'Sequencing QC', ['Read Group Metrics'], ['FastQC'], ['FastQC']],
@@ -285,8 +285,8 @@ def main():
     parser.add_argument("-b", "--genome_build", dest="genome_build", default="GRCh38_hla_decoy_ebv", help="RNA-Seq alignment genome build")
     parser.add_argument("-w", "--wf_name", dest="wf_name", required=True, help="Workflow name")
     parser.add_argument("-v", "--wf_version", dest="wf_version", required=True, help="Workflow version")
-    parser.add_argument("-r", "--wf_run", dest="wf_run", required=True, help="workflow run ID")
-    parser.add_argument("-s", "--wf_session", dest="wf_session", required=True, help="workflow session ID")
+    parser.add_argument("-r", "--wf_run", dest="wf_run", required=True, help="Workflow run ID")
+    parser.add_argument("-s", "--wf_session", dest="wf_session", required=True, help="Workflow session ID")
     args = parser.parse_args()
 
     with open(args.seq_experiment_analysis, 'r') as f:

payload-gen-rna-alignment/tests/expected/expected.test-job-1.out.json

@@ -8,8 +8,8 @@
     "workflow_version": "0.1.0",
     "genome_build": "GRCh38_hla_decoy_ebv",
     "genome_annotation": "GENCODE v38",
-    "run_id": "exotic_darwin",
-    "session_id": "1c2b7b63-3b5f-40e2-a6b2-3dcd9d71217c",
+    "run_id": "insane_hugle",
+    "session_id": "67ccf9ba-915e-4dda-ac5c-975fd1ff0509",
     "inputs": [
       {
         "analysis_type": "sequencing_experiment",
@@ -71,7 +71,7 @@
   "experiment": {
     "submitter_sequencing_experiment_id": "TEST_EXP",
     "sequencing_center": "SIM",
-    "platform": "Simulation",
+    "platform": "ILLUMINA",
     "platform_model": "Polyester",
     "experimental_strategy": "RNA-Seq",
     "sequencing_date": "2021-04-21"

payload-gen-rna-alignment/tests/expected/expected.test-job-2.out.json

@@ -8,8 +8,8 @@
     "workflow_version": "0.1.0",
     "genome_build": "GRCh38_hla_decoy_ebv",
     "genome_annotation": "GENCODE v38",
-    "run_id": "amazing_keller",
-    "session_id": "e281fe1b-8b46-4b77-a1f1-349ad53b76e3",
+    "run_id": "ridiculous_bhaskara",
+    "session_id": "b2c42a90-fb78-4ba3-8a02-0bb02dfbf309",
     "inputs": [
       {
         "analysis_type": "sequencing_experiment",
@@ -64,7 +64,7 @@
         },
         "description": "RNA alignment metrics for a SAM or BAM file."
       },
-      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211014.star.collectrnaseqmetrics.tgz",
+      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.star.collectrnaseqmetrics.tgz",
       "dataType": "Aligned Reads QC"
     },
     {
@@ -98,7 +98,7 @@
           ]
         }
       },
-      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211014.star.duplicates_metrics.tgz",
+      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.star.duplicates_metrics.tgz",
       "dataType": "Aligned Reads QC"
     },
     {
@@ -132,7 +132,7 @@
         },
         "description": "High level sequencing reads QC metrics generated by FastQC."
       },
-      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211014.S01L1.fastqc.tgz",
+      "fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.S01L1.fastqc.tgz",
       "dataType": "Sequencing QC"
     }
   ],
@@ -156,7 +156,7 @@
   "experiment": {
     "submitter_sequencing_experiment_id": "TEST_EXP",
     "sequencing_center": "SIM",
-    "platform": "Simulation",
+    "platform": "ILLUMINA",
     "platform_model": "Polyester",
     "experimental_strategy": "RNA-Seq",
     "sequencing_date": "2021-04-21"

tests/data/s3.881fe6cf-8c80-4c7b-9f4d-b8dac9601d01.sequencing_experiment.payload.json

@@ -6,7 +6,7 @@
   "experiment": {
     "submitter_sequencing_experiment_id": "TEST_EXP",
     "sequencing_center": "SIM",
-    "platform": "Simulation",
+    "platform": "ILLUMINA",
     "platform_model": "Polyester",
     "experimental_strategy": "RNA-Seq",
     "sequencing_date": "2021-04-21"