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oops forgot to revert thread_count thing
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gesinaphillips committed Oct 24, 2024
1 parent 32f3f36 commit aeaeeae
Showing 1 changed file with 3 additions and 6 deletions.
9 changes: 3 additions & 6 deletions src/ingest_validation_tests/fastq_validator.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
from os import cpu_count
from typing import List, Optional

from fastq_validator_logic import FASTQValidatorLogic, _log
Expand All @@ -8,14 +9,10 @@ class FASTQValidator(Validator):
description = "Check FASTQ files for basic syntax and consistency."
cost = 15.0
version = "1.0"
# need to add to parent validator class in IVT, hack for now
thread_count = None

def collect_errors(self, **kwargs) -> List[Optional[str]]:
del kwargs
if not self.thread_count:
self.thread_count = 1
_log(f"Threading at FastQValidator with {self.thread_count}")
threads = kwargs.get("coreuse", None) or cpu_count() // 4 or 1
_log(f"Threading at FastQValidator with {threads}")
validator = FASTQValidatorLogic(verbose=True)
validator.validate_fastq_files_in_path(self.paths, self.thread_count)
if validator.errors:
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