RBT COLLAPSE-READS-TO-FRAGMENTS BAM

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/rbt/collapse_reads_to_fragments-bam?label=version%20update%20pull%20requests

Calculate consensus reads from read groups marked by PicardTools MarkDuplicates or UmiAwareMarkDuplicatesWithMateCigar.

URL: https://github.com/rust-bio/rust-bio-tools

Example

This wrapper can be used in the following way:

rule calc_consensus_reads:
    input:
        "mapped/{sample}.marked.bam",
    output:
        consensus_r1="results/consensus/{sample}.1.fq",
        consensus_r2="results/consensus/{sample}.2.fq",
        consensus_se="results/consensus/{sample}.se.fq",
        skipped="results/consensus/{sample}.skipped.bam",
    params:
        extra="--annotate-record-ids",
    log:
        "logs/consensus/{sample}.log",
    wrapper:
        "v3.8.0-1-g149ef14/bio/rbt/collapse_reads_to_fragments-bam"

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

  • rust-bio-tools=0.42.0

Authors

  • Felix Mölder

Code

__author__ = "Felix Mölder"
__copyright__ = "Copyright 2022, Felix Mölder"
__email__ = "felix.moelder@uk-essen.de"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

extra = snakemake.params.get("extra", "")

shell(
    "rbt collapse-reads-to-fragments bam {extra} {snakemake.input[0]} {snakemake.output} {log}"
)