FASTQC

Generate fastq qc statistics using fastqc.

Software dependencies

  • fontconfig ==2.12.1
  • fastqc ==0.11.5

Example

This wrapper can be used in the following way:

rule fastqc:
    input:
        "reads/{sample}.fastq"
    output:
        html="qc/{sample}.html",
        zip="qc/{sample}.zip"
    params: ""
    wrapper:
        "0.18.0/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 snakemake.shell import shell


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.
output_dir = path.dirname(snakemake.output.html)

shell("fastqc {snakemake.params} --quiet "
      "--outdir {output_dir} {snakemake.input[0]}")

# Move outputs into proper position.
output_base = basename_without_ext(snakemake.input[0])
html_path = path.join(output_dir, output_base + "_fastqc.html")
zip_path = path.join(output_dir, 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}")