S000

Author: antgonza

src/qp_klp/PacBioMetagenomicWorkflow.py

@@ -40,7 +40,7 @@ def __init__(self, **kwargs):
 
         samples = [
             {'barcode': sample['barcode_id'],
-             'sample_name': sample['Sample_Name'],
+             'sample_name': sample['Sample_ID'],
              'project_name': sample['Sample_Project'],
              'lane': sample['Lane']}
             for sample in self.pipeline.sample_sheet.samples]

src/qp_klp/scripts/pacbio_commands.py

@@ -36,8 +36,9 @@ def generate_bam2fastq_commands(sample_list, run_folder, outdir, threads):
             missing_files.append(bc)
             continue
         od = f'{outdir}/{pn}'
+
         makedirs(od, exist_ok=True)
-        fn = f'{od}/{sn}_L00{lane}_R1_001'
+        fn = f'{od}/{sn}_S000_L00{lane}_R1_001'
         cmd = (f'bam2fastq -j {threads} -o {fn} -c 9 '
                f'{files[bc]}; '
                f'fqtools count {fn}.fastq.gz > '