CHOPPER

chopper from nanopack.

URL: https://github.com/wdecoster/chopper

Example

This wrapper can be used in the following way:

test/Snakefile not found.

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• chopper

Input/Output

Input:

• fastqs: input fastq files list, can be gziped.(such as, fastq, fastq.gz, fq, fq.gz). All file must be the same file type.

Output:

• out: filtered fastq file, same as the input.

Params

• chopper: path to chopper, (optional). default is chopper.

• quality: minimum Phred average quality score. (optional), default is 0.

• min_len: filter on minimum read length (optional). default is 1.

• max_len: filter on maximum read length (optional). default is 2147483647.

• headcrop: Trim N nucleotides from the start of a read. (optional), default is 0.

• tailcrop: Trim N nucleotides from the end of a read. (optional), default is 0.

• extras: extra arguments to chopper (optional).

Authors

• yangqun

Code

# chopper from nanopack.
__author__ = "yangqun"

import os
import sys

from snakemake.shell import shell

# params.
if 'fastqs' not in snakemake.input.keys():
    sys.exit("fastqs must be given.")
if 'out' not in snakemake.output.keys():
    sys.exit('out must be given.')

fastqs = snakemake.input.get('fastqs')
out = snakemake.output.get('out')

# check input file extension.
exts = set([os.path.splitext(x)[-1] for x in fastqs])
if len(exts) > 1:
    sys.exit('input file must be only 1 file type.')

ext = exts.pop()
ext = ext.lower()

# optional params
chopper = snakemake.params.get('chopper', 'chopper')
quality = snakemake.params.get('quality', '0')
min_len = snakemake.params.get('min_len', '1')
max_len = snakemake.params.get('max_len', '2147483647')
headcrop = snakemake.params.get('headcrop', '0')
tailcrop = snakemake.params.get('tailcrop', '0')
extras = snakemake.params.get('extras', '')

# commands.
if ext == '.gz':
    input_cmd = 'zcat {}'.format(' '.join(fastqs))
else:
    input_cmd = 'cat {}'.format(' '.join(fastqs))

out_cmd = f' | gzip >{out}' if out.endswith('.gz') else f' >{out}'
threads_cmd = f'--threads {snakemake.threads}'

shell(
    "{input_cmd} "
    "| {chopper} {threads_cmd} --maxlength {max_len} --minlength {min_len} "
    "--headcrop {headcrop} --tailcrop {tailcrop} --quality {quality} "
    "{out_cmd}"
)