del raw_reverse_seqs

Author: antgonza

src/qp_klp/PacBioMetagenomicWorkflow.py

@@ -26,7 +26,6 @@ def __init__(self, **kwargs):
         if 'overwrite_prep_with_original' in self.kwargs:
             self.overwrite_prep_with_original = \
                 self.kwargs['overwrite_prep_with_original']
-        self.files_regex = 'long_read'
         self.pipeline = Pipeline(self.kwargs['config_fp'],
                                  self.kwargs['run_identifier'],
                                  self.kwargs['uif_path'],

src/qp_klp/Workflows.py

@@ -8,6 +8,7 @@
 import logging
 from shutil import rmtree
 from .Assays import ASSAY_NAME_AMPLICON
+from metapool.sample_sheet import PROTOCOL_NAME_PACBIO_SMRT
 from sequence_processing_pipeline.util import determine_orientation
 
 
@@ -600,6 +601,10 @@ def _get_postqc_fastq_files(self, out_dir, project):
         if self.pipeline.pipeline_type != ASSAY_NAME_AMPLICON:
             del (files['raw_barcodes'])
 
+        # PacBio doesn't have reverse reads
+        if self.protocol_type == PROTOCOL_NAME_PACBIO_SMRT:
+            del (files['raw_reverse_seqs'])
+
         # confirm expected lists of reads are not empty.
         for f_type in files:
             if not files[f_type]:

src/sequence_processing_pipeline/util.py

@@ -32,12 +32,6 @@
         'html': REC(r'^(.*).html$'),
         'json':  REC(r'^(.*).json$')
     },
-    'long_read': {
-        'fastq': REC(r'^(.*)_R1.fastq\.gz$'),
-        'interleave_fastq': REC(r'^(.*)_R1.interleave\.fastq\.gz$'),
-        'html': REC(r'^(.*)_R1.html$'),
-        'json':  REC(r'^(.*)_R1.json$')
-    },
 }
 
 

tests/test_PacBioWorflow.py

@@ -13,7 +13,7 @@
 from shutil import rmtree
 from pathlib import Path
 import pandas as pd
-from metapool.sample_sheet import (PROTOCOL_NAME_PACBIO_SMRT)
+from metapool.sample_sheet import PROTOCOL_NAME_PACBIO_SMRT
 from sequence_processing_pipeline.PipelineError import PipelineError
 from qp_klp.Assays import ASSAY_NAME_METAGENOMIC
 from qiita_client.testing import PluginTestCase