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Commit e0208acd authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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adds snakemake wrapper of 0.64.0/bio/multiqc- #47

parent 17453fc5
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2 merge requests!5Explicit conda env,!4User configurable hardware resources
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- multiqc ==1.9
name: multiqc
description: |
Generate qc report using multiqc.
authors:
- Julian de Ruiter
input:
- input directory containing qc files
output:
- qc report (html)
"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from os import path
from snakemake.shell import shell
input_dirs = set(path.dirname(fp) for fp in snakemake.input)
output_dir = path.dirname(snakemake.output[0])
output_name = path.basename(snakemake.output[0])
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"multiqc"
" {snakemake.params}"
" --force"
" -o {output_dir}"
" -n {output_name}"
" {input_dirs}"
" {log}"
)
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