SAMBAMBA MERGE¶
merge multiple BAM files into one using `sambamba https://lomereiter.github.io/sambamba/docs/sambamba-merge.html`_
Example¶
This wrapper can be used in the following way:
rule sambamba_merge:
input:
["mapped/{sample}_1.sorted.bam", "mapped/{sample}_2.sorted.bam"]
output:
"mapped/{sample}.merged.bam"
params:
extra="" # optional parameters
log:
"logs/sambamba-merge/{sample}.log"
threads: 1
wrapper:
"v1.12.2/bio/sambamba/merge"
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¶
sambamba==0.8.0
Authors¶
- Jan Forster
Code¶
__author__ = "Jan Forster"
__copyright__ = "Copyright 2021, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"
import os
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"sambamba merge {snakemake.params.extra} -t {snakemake.threads} "
"{snakemake.output[0]} {snakemake.input} "
"{log}"
)