Rename "hivseqinr_results_tar" argument to "detailed_results_tar"

Singularity

@@ -13,7 +13,7 @@ From: ubuntu:22.04
     MAINTAINER BC CfE in HIV/AIDS https://github.com/cfe-lab/
     KIVE_INPUTS sample_info_csv contigs_csv conseqs_csv cascade_csv
     KIVE_OUTPUTS outcome_summary_csv conseqs_primers_csv contigs_primers_csv \
-        table_precursor_csv proviral_landscape_csv hivseqinr_results_tar
+        table_precursor_csv proviral_landscape_csv detailed_results_tar
     KIVE_THREADS 1
     KIVE_MEMORY 6000
 

gene_splicer/sample.py

@@ -43,7 +43,7 @@ def parse_args():
     parser.add_argument('proviral_landscape_csv',
                         help='Data for proviral landscape plot',
                         type=FileType('w'))
-    parser.add_argument('hivseqinr_results_tar',
+    parser.add_argument('detailed_results_tar',
                         help="Archive file with HIVSeqinR's final results "
                              "folder, or HIVIntact's results.",
                         type=FileType('wb'))
@@ -73,7 +73,7 @@ def parse_args():
         help='To avoid memory issues in hivseqinr, split the resulting '
              'qc-passed sequences into this number of fastas, each will be '
              'processed sequentially and then all will be merged into the '
-             'final result')
+             'final result. Obsolete for HIVIntact.')
     return parser.parse_args()
 
 
@@ -94,9 +94,9 @@ def main():
     run_name = sample_info.get('run_name', 'kive_run')
     if args.hivintact:
         hivseqinr_results_tar = None
-        hivintact_results_tar = args.hivseqinr_results_tar
+        hivintact_results_tar = args.detailed_results_tar
     else:
-        hivseqinr_results_tar = args.hivseqinr_results_tar
+        hivseqinr_results_tar = args.detailed_results_tar
         hivintact_results_tar = None
     fasta_files = primer_finder.run(contigs_csv=args.contigs_csv,
                                     conseqs_csv=args.conseqs_csv,