fix: ignore jid tracking if local execution

dmux

@@ -42,10 +42,14 @@ def run(args):
         demux_runs = runs
         for i, (rundir, run_infos) in enumerate(demux_runs):
             run_infos['demux_dir'] = config['out_to'][i]
-            run_infos['parent_jid'] = jids[i]
+            if args.local:
+                run_infos['parent_jid'] = None
+            else
+                run_infos['parent_jid'] = jids[i]
         ngsqc(args, demux_runs=demux_runs)
 
 
+
 def ngsqc(args, demux_runs=False):
     """
     Front-end sub-command for NGS QA/QC pipeline analysis.
@@ -83,7 +87,7 @@ def ngsqc(args, demux_runs=False):
         sample_sheet = run_info['samplesheet']
         configs['sample_sheet'].append(str(sample_sheet.path.absolute()))
         configs['projects'].append(sample_sheet.samples[0].Sample_Project)
-        if 'parent_jid' in run_info:
+        if 'parent_jid' in run_info and not args.local:
             configs['parent_jid'].append(run_info['parent_jid'])
         sample_list = [
             dict(sid=sample.Sample_ID+'_S'+str(i), r1_adapter=sample.index, r2_adapter=sample.index2) 

scripts/utils.py

@@ -348,7 +348,7 @@ def exec_ngsqc_pipeline(configs, dry_run=False, local=False):
         config_file = Path(this_config['out_to'], '.config', f'config_job_{str(i)}.json').absolute()
         json.dump(this_config, open(config_file, 'w'), cls=PathJSONEncoder, indent=4)
         top_env = {}
-        if 'parent_jid' in this_config and this_config['parent_jid'] is not None:
+        if 'parent_jid' in this_config and this_config['parent_jid'] is not None and not local:
             top_env['SLURM_DEP_PARENT_JOB'] = str(this_config['parent_jid'])
         top_env['PATH'] = os.environ["PATH"]
         top_env['SNK_CONFIG'] = str(config_file.absolute())