Commit c2d34887 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files remove hard-coded options, add --pear-options

Specific PEAR options should be configured through pre-process configs.
parent 8a114b5e
......@@ -5,14 +5,16 @@ import shutil
import gzip
import subprocess
import argparse
import shlex
parser = argparse.ArgumentParser(description='Use pear read merger to make a new fastq file and keep unmerged reads')
parser = argparse.ArgumentParser(description='Use PEAR read merger to make a new fastq file and keep unmerged reads')
parser.add_argument("file_R1", help="reverse read file")
parser.add_argument("file_R2", help="forward read file")
parser.add_argument("output_file", help="output file")
parser.add_argument("-r1", "--keep_r1", help="keep unmerged reverse reads", action="store_true")
parser.add_argument("-r2", "--keep_r2", help="keep unmerged forward reads", action="store_true")
parser.add_argument("-p", "--pear-options", help="additional options passed to PEAR", default="")
args = parser.parse_args()
......@@ -25,9 +27,9 @@["pear",
"-f", f_r1,
"-r", f_r2,
"-o", f_out,
"-n", "100",
"-m", "490",
"-j", "1"])
"-j", "1"]
+ shlex.split(args.pear_options)
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