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Commit 85ae9db4 authored by Bertache's avatar Bertache
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Fix num_processes

parent b2c6fa67
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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. Open output files for writing with pigz compression.
Parameters: 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_forward (str): Path to the forward output file.
output_reverse (str): Path to the reverse output file. output_reverse (str): Path to the reverse output file.
...@@ -14,15 +14,15 @@ def open_output(output_forward, output_reverse, num_processes): ...@@ -14,15 +14,15 @@ def open_output(output_forward, output_reverse, num_processes):
import signal import signal
import subprocess import subprocess
from auxiliary import signal_handler from auxiliary import signal_handler
num_processes = int(num_processes/2) write_processes = int(write_processes/2)
# Open output files for writing # Open output files for writing
out_f = subprocess.Popen( out_f = subprocess.Popen(
args=["pigz", "-c", "-p", str(num_processes)], args=["pigz", "-c", "-p", str(write_processes)],
stdin=subprocess.PIPE, stdin=subprocess.PIPE,
stdout=open(file=output_forward, mode="wt"), stdout=open(file=output_forward, mode="wt"),
) )
out_r = subprocess.Popen( out_r = subprocess.Popen(
["pigz", "-c", "-p", str(num_processes)], ["pigz", "-c", "-p", str(write_processes)],
stdin=subprocess.PIPE, stdin=subprocess.PIPE,
stdout=open(file=output_reverse, mode="wt"), stdout=open(file=output_reverse, mode="wt"),
) )
...@@ -38,7 +38,7 @@ def open_output(output_forward, output_reverse, num_processes): ...@@ -38,7 +38,7 @@ def open_output(output_forward, output_reverse, num_processes):
) )
return out_f, out_r 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. 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): ...@@ -49,7 +49,7 @@ def write_fastq_pair(output_queue, output_forward, output_reverse, num_process):
num_process (int): Number of fragmenting threads. num_process (int): Number of fragmenting threads.
""" """
import sys 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: while num_process > 0:
try: try:
data = output_queue.get() data = output_queue.get()
......
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