MULTIQC¶
Generate qc report using multiqc.
Software dependencies¶
- multiqc ==1.2
- networkx <2.0
Example¶
This wrapper can be used in the following way:
rule multiqc:
input:
expand("samtools_stats/{sample}.txt", sample=["a", "b"])
output:
"qc/multiqc.html"
params:
"" # Optional: extra parameters for multiqc.
log:
"logs/multiqc.log"
wrapper:
"0.19.1/bio/multiqc"
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.
Authors¶
- Julian de Ruiter
Code¶
"""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}")