DEDUPLICATE_BISMARK

Deduplicate Bismark Bam Files

URL: https://github.com/FelixKrueger/Bismark/

Example

This wrapper can be used in the following way:

rule deduplicate_bismark:
    input: "bams/{sample}.bam"
    output:
        bam="bams/{sample}.deduplicated.bam",
        report="bams/{sample}.deduplication_report.txt",
    log:
        "logs/bams/{sample}.deduplicated.log",
    params:
        extra=""  # optional params string
    wrapper:
        "v3.8.0/bio/bismark/deduplicate_bismark"

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.

Software dependencies

• bismark=0.24.2

• bowtie2=2.5.3

• samtools=1.19.2

Input/Output

Input:

• path to one or multiple *.bam files aligned by Bismark, if multiple passed ‘–multiple’ argument will be added automatically.

Output:

• bam: Result bam file path. The file will be renamed if differs from NAME.deduplicated.bam for given ‘NAME.bam’ input.

• report: Result report path. The file will be renamed if differs from NAME.deduplication_report.txt for given ‘NAME.bam’ input.

Params

• extra: Additional deduplicate_bismark args

Authors

• Roman Cherniatchik

Code

"""Snakemake wrapper for Bismark aligned reads deduplication using deduplicate_bismark."""

# https://github.com/FelixKrueger/Bismark/blob/master/deduplicate_bismark

__author__ = "Roman Chernyatchik"
__copyright__ = "Copyright (c) 2019 JetBrains"
__email__ = "roman.chernyatchik@jetbrains.com"
__license__ = "MIT"

import os
from snakemake.shell import shell

bam_path = snakemake.output.get("bam", None)
report_path = snakemake.output.get("report", None)
if not bam_path or not report_path:
    raise ValueError(
        "bismark/deduplicate_bismark: Please specify both 'bam=..' and 'report=..' paths in output section"
    )

output_dir = os.path.dirname(bam_path)
if output_dir != os.path.dirname(report_path):
    raise ValueError(
        "bismark/deduplicate_bismark: BAM and Report files expected to have the same parent directory"
        " but was {} and {}".format(bam_path, report_path)
    )

arg_output_dir = "--output_dir '{}'".format(output_dir) if output_dir else ""
arg_multiple = "--multiple" if len(snakemake.input) > 1 else ""

params_extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
log_append = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
shell(
    "deduplicate_bismark {params_extra} --bam {arg_multiple}"
    " {arg_output_dir} {snakemake.input} {log}"
)

# Move outputs into proper position.
fst_input_filename = os.path.basename(snakemake.input[0])
fst_input_basename = os.path.splitext(fst_input_filename)[0]
prefix = os.path.join(output_dir, fst_input_basename)

deduplicated_bam_actual_name = prefix + ".deduplicated.bam"
if arg_multiple:
    # bismark does it exactly like this:
    deduplicated_bam_actual_name = deduplicated_bam_actual_name.replace(
        "deduplicated", "multiple.deduplicated", 1
    )

expected_2_actual_paths = [
    (bam_path, deduplicated_bam_actual_name),
    (
        report_path,
        prefix + (".multiple" if arg_multiple else "") + ".deduplication_report.txt",
    ),
]
for exp_path, actual_path in expected_2_actual_paths:
    if exp_path and (exp_path != actual_path):
        shell("mv {actual_path:q} {exp_path:q} {log_append}")