BISMARK2REPORT

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Generate graphical HTML report from Bismark reports (see https://github.com/FelixKrueger/Bismark/blob/master/bismark2report).

Example

This wrapper can be used in the following way:

# Example: Pair-ended reads
rule bismark2report_pe:
    input:
        alignment_report="bams/{sample}_{genome}_PE_report.txt",
        nucleotide_report="bams/{sample}_{genome}_pe.nucleotide_stats.txt",
        dedup_report="bams/{sample}_{genome}_pe.deduplication_report.txt",
        mbias_report="meth/{sample}_{genome}_pe.deduplicated.M-bias.txt",
        splitting_report="meth/{sample}_{genome}_pe.deduplicated_splitting_report.txt"
    output:
        html="qc/meth/{sample}_{genome}.bismark2report.html",
    log:
        "logs/qc/meth/{sample}_{genome}.bismark2report.html.log",
    params:
        skip_optional_reports=True
    wrapper:
        "v3.10.2/bio/bismark/bismark2report"

# Example: Single-ended reads
rule bismark2report_se:
    input:
        alignment_report="bams/{sample}_{genome}_SE_report.txt",
        nucleotide_report="bams/{sample}_{genome}.nucleotide_stats.txt",
        dedup_report="bams/{sample}_{genome}.deduplication_report.txt",
        mbias_report="meth/{sample}_{genome}.deduplicated.M-bias.txt",
        splitting_report="meth/{sample}_{genome}.deduplicated_splitting_report.txt"
    output:
        html="qc/meth/{sample}_{genome}.bismark2report.html",
    log:
        "logs/qc/meth/{sample}_{genome}.bismark2report.html.log",
    params:
        skip_optional_reports=True
    wrapper:
        "v3.10.2/bio/bismark/bismark2report"

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

  • bowtie2=2.5.3

  • bismark=0.24.2

  • samtools=1.20

Input/Output

Input:

  • alignment_report: Alignment report (if not specified bismark will try to find it current directory)

  • nucleotide_report: Optional Bismark nucleotide coverage report (if not specified bismark will try to find it current directory)

  • dedup_report: Optional deduplication report (if not specified bismark will try to find it current directory)

  • splitting_report: Optional Bismark methylation extractor report (if not specified bismark will try to find it current directory)

  • mbias_report: Optional Bismark methylation extractor report (if not specified bismark will try to find it current directory)

Output:

  • html: Output HTML file path, if batch mode isn’t used.

  • html_dir: Output dir path for HTML reports if batch mode is used

Params

  • skip_optional_reports: Use ‘true’ of ‘false’ to not look for optional reports not mentioned in input section (passes ‘none’ to bismark2report)

  • extra: Any additional args

Authors

  • Roman Cherniatchik

Code

"""Snakemake wrapper to generate graphical HTML report from Bismark reports."""

# https://github.com/FelixKrueger/Bismark/blob/master/bismark2report

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

import os
from snakemake.shell import shell


def answer2bool(v):
    return str(v).lower() in ("yes", "true", "t", "1")


extra = snakemake.params.get("extra", "")
cmds = ["bismark2report {extra}"]

# output
html_file = snakemake.output.get("html", "")
output_dir = snakemake.output.get("html_dir", None)
if output_dir is None:
    if html_file:
        output_dir = os.path.dirname(html_file)
else:
    if html_file:
        raise ValueError(
            "bismark/bismark2report: Choose one: 'html=...' for a single dir or 'html_dir=...' for batch processing."
        )

if output_dir is None:
    raise ValueError(
        "bismark/bismark2report: Output file or directory not specified. "
        "Use 'html=...' for a single dir or 'html_dir=...' for batch "
        "processing."
    )

if output_dir:
    cmds.append("--dir {output_dir:q}")

if html_file:
    html_file_name = os.path.basename(html_file)
    cmds.append("--output {html_file_name:q}")

# reports
reports = [
    "alignment_report",
    "dedup_report",
    "splitting_report",
    "mbias_report",
    "nucleotide_report",
]
skip_optional_reports = answer2bool(
    snakemake.params.get("skip_optional_reports", False)
)
for report_name in reports:
    path = snakemake.input.get(report_name, "")
    if path:
        locals()[report_name] = path
        cmds.append("--{0} {{{1}:q}}".format(report_name, report_name))
    elif skip_optional_reports:
        cmds.append("--{0} 'none'".format(report_name))

# log
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
cmds.append("{log}")

# run shell command:
shell(" ".join(cmds))