From 85ae9db4af3cfa473c5ee68f34f9b9f04d51fa6a Mon Sep 17 00:00:00 2001
From: Bertache <samir.bertache@etu.uca.fr>
Date: Thu, 3 Apr 2025 14:24:13 +0200
Subject: [PATCH] Fix num_processes
---
microsplit/fastq.py | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/microsplit/fastq.py b/microsplit/fastq.py
index 9fc154c..d23c263 100644
--- a/microsplit/fastq.py
+++ b/microsplit/fastq.py
@@ -1,9 +1,9 @@
-def open_output(output_forward, output_reverse, num_processes):
+def open_output(output_forward, output_reverse, write_processes):
"""
Open output files for writing with pigz compression.
Parameters:
- num_processes (int): Number of threads for writing.
+ write_processes (int): Number of threads for writing.
output_forward (str): Path to the forward output file.
output_reverse (str): Path to the reverse output file.
@@ -14,15 +14,15 @@ def open_output(output_forward, output_reverse, num_processes):
import signal
import subprocess
from auxiliary import signal_handler
- num_processes = int(num_processes/2)
+ write_processes = int(write_processes/2)
# Open output files for writing
out_f = subprocess.Popen(
- args=["pigz", "-c", "-p", str(num_processes)],
+ args=["pigz", "-c", "-p", str(write_processes)],
stdin=subprocess.PIPE,
stdout=open(file=output_forward, mode="wt"),
)
out_r = subprocess.Popen(
- ["pigz", "-c", "-p", str(num_processes)],
+ ["pigz", "-c", "-p", str(write_processes)],
stdin=subprocess.PIPE,
stdout=open(file=output_reverse, mode="wt"),
)
@@ -38,7 +38,7 @@ def open_output(output_forward, output_reverse, num_processes):
)
return out_f, out_r
-def write_fastq_pair(output_queue, output_forward, output_reverse, num_process):
+def write_fastq_pair(output_queue, output_forward, output_reverse, num_process, write_processes):
"""
Write FastQ file pairs to the output using data from the output queue.
@@ -49,7 +49,7 @@ def write_fastq_pair(output_queue, output_forward, output_reverse, num_process):
num_process (int): Number of fragmenting threads.
"""
import sys
- out_f, out_r = open_output(output_forward, output_reverse, num_process)
+ out_f, out_r = open_output(output_forward, output_reverse, write_processes)
while num_process > 0:
try:
data = output_queue.get()
--
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