QUALIMAP BAMQC

Run qualimap bamqc to create a QC report for aligned NGS data data. It can be used for WGS, WES, RNA, ChIP-Seq, etc.

URL: http://qualimap.conesalab.org/doc_html/analysis.html#bam-qc

Example

This wrapper can be used in the following way:

rule qualimap:
    input:
        # BAM aligned, splicing-aware, to reference genome
        bam="mapped/a.bam",
    output:
        directory("qc/a"),
    log:
        "logs/qualimap/bamqc/a.log",
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=4096,
    wrapper:
        "v7.6.0/bio/qualimap/bamqc"

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.

Notes

• The extra param allows for additional program arguments.

Software dependencies

• qualimap=2.3

• snakemake-wrapper-utils=0.8.0

Input/Output

Input:

• BAM file of data aligned to genome

Output:

• QC report in TXT format (genome_results.txt)

Authors

• Fritjof Lammers

• Brett Copeland

Code

__author__ = "Fritjof Lammers, Christopher Schröder"
__copyright__ = "Copyright 2022, Fritjof Lammers"
__email__ = "f.lammers@dkfz.de"

__license__ = "MIT"


import os
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

# Set JAVA options
java_opts = get_java_opts(snakemake)
if java_opts:
    java_opts_str = f'JAVA_OPTS="{java_opts}"'
else:
    java_opts_str = ""

# unset DISPLAY environment variable to avoid X11 error message issued by qualimap
if os.environ.get("DISPLAY"):
    del os.environ["DISPLAY"]

if target := snakemake.input.get("target", ""):
    target = f"--feature-file {target}"

shell(
    "{java_opts_str} qualimap bamqc"
    " -nt {snakemake.threads}"
    " -bam {snakemake.input.bam}"
    " {target}"
    " {extra}"
    " -outdir {snakemake.output}"
    " {log}"
)