self.files_regex = long_read

Author: antgonza

src/qp_klp/Assays.py

@@ -494,6 +494,7 @@ def qc_reads(self):
         # is not defined, just fallback to the SPP expected default regex
         if not hasattr(self, 'files_regex'):
             self.files_regex = 'SPP'
+
         # base quality control used by multiple Assay types.
         job = NuQCJob(self.raw_fastq_files_path,
                       self.pipeline.output_path,

src/qp_klp/PacBioMetagenomicWorkflow.py

@@ -26,10 +26,7 @@ def __init__(self, **kwargs):
         if 'overwrite_prep_with_original' in self.kwargs:
             self.overwrite_prep_with_original = \
                 self.kwargs['overwrite_prep_with_original']
-        if 'files_regex' in self.kwargs:
-            self.files_regex = self.kwargs['files_regex']
-        else:
-            self.files_regex = 'SPP'
+        self.files_regex = 'long_read'
         self.pipeline = Pipeline(self.kwargs['config_fp'],
                                  self.kwargs['run_identifier'],
                                  self.kwargs['uif_path'],

src/sequence_processing_pipeline/util.py

@@ -4,8 +4,8 @@
 
 PAIR_UNDERSCORE = (REC(r'_R1_'), '_R1_', '_R2_')
 PAIR_DOT = (REC(r'\.R1\.'), '.R1.', '.R2.')
-SIMPLE_PAIR_UNDERSCAOTE = (REC(r'_R1'), '_R1', '_R2')
-PAIR_TESTS = (PAIR_UNDERSCORE, PAIR_DOT, SIMPLE_PAIR_UNDERSCAOTE)
+SIMPLE_PAIR_UNDERSCORE = (REC(r'_R1'), '_R1', '_R2')
+PAIR_TESTS = (PAIR_UNDERSCORE, PAIR_DOT, SIMPLE_PAIR_UNDERSCORE)
 FILES_REGEX = {
     'SPP': {
         'fastq': REC(r'^(.*)_S\d{1,4}_L\d{3}_R\d_\d{3}\.fastq\.gz$'),
@@ -32,6 +32,12 @@
         'html': REC(r'^(.*).html$'),
         '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

@@ -54,7 +54,7 @@ def _inject_data(self, wf):
         fastqc_dir = f'{self.output_dir}/FastQCJob/logs/'
         multiqc_dir = f'{self.output_dir}/MultiQCJob/logs/'
         genprep_dir = (f'{self.output_dir}/GenPrepFileJob/'
-                       '211021_A00000_0000_SAMPLE/')
+                       'r11111_20250101_111111/')
         makedirs(nuqc_dir, exist_ok=True)
         makedirs(fastqc_dir, exist_ok=True)
         makedirs(multiqc_dir, exist_ok=True)