FASTQC¶
Generate fastq qc statistics using fastqc.
Software dependencies¶
- fastqc ==0.11.8
Example¶
This wrapper can be used in the following way:
rule fastqc:
input:
"reads/{sample}.fastq"
output:
html="qc/fastqc/{sample}.html",
zip="qc/fastqc/{sample}.zip"
params: ""
log:
"logs/fastqc/{sample}.log"
wrapper:
"0.32.0/bio/fastqc"
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 fastqc."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from os import path
from tempfile import TemporaryDirectory
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
def basename_without_ext(file_path):
"""Returns basename of file path, without the file extension."""
base = path.basename(file_path)
split_ind = 2 if base.endswith(".gz") else 1
base = ".".join(base.split(".")[:-split_ind])
return base
# Run fastqc, since there can be race conditions if multiple jobs
# use the same fastqc dir, we create a temp dir.
with TemporaryDirectory() as tempdir:
shell("fastqc {snakemake.params} --quiet "
"--outdir {tempdir} {snakemake.input[0]}"
" {log}")
# Move outputs into proper position.
output_base = basename_without_ext(snakemake.input[0])
html_path = path.join(tempdir, output_base + "_fastqc.html")
zip_path = path.join(tempdir, output_base + "_fastqc.zip")
if snakemake.output.html != html_path:
shell("mv {html_path} {snakemake.output.html}")
if snakemake.output.zip != zip_path:
shell("mv {zip_path} {snakemake.output.zip}")