1"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
2# Snakemake wrappers are provided by Truwl to teach the internal mechanics of Snakemake recipes. View https://github.com/snakemake/snakemake-wrappers to learn how to use wrappers.
3
4__author__ = "Julian de Ruiter"
5__copyright__ = "Copyright 2017, Julian de Ruiter"
6__email__ = "julianderuiter@gmail.com"
7__license__ = "MIT"
8
9
10from os import path
11
12from snakemake.shell import shell
13
14
15input_dirs = set(path.dirname(fp) for fp in snakemake.input)
16output_dir = path.dirname(snakemake.output[0])
17output_name = path.basename(snakemake.output[0])
18log = snakemake.log_fmt_shell(stdout=True, stderr=True)
19
20shell(
21    "multiqc"
22    " {snakemake.params}"
23    " --force"
24    " -o {output_dir}"
25    " -n {output_name}"
26    " {input_dirs}"
27    " {log}"
28)
29