SAMBAMBA INDEX
Indexing a bam file with `sambamba https://lomereiter.github.io/sambamba/docs/sambamba-index.html`_
Example
This wrapper can be used in the following way:
rule sambamba_index:
input:
"mapped/{sample}.bam"
output:
"mapped/{sample}.bam.bai"
params:
extra="" # optional parameters
log:
"logs/sambamba-index/{sample}.log"
threads: 8
wrapper:
"v3.3.6/bio/sambamba/index"
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=1.0
Input/Output
Input:
bam file
Output:
bam index
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 index {snakemake.params.extra} -t {snakemake.threads} "
"{snakemake.input[0]} {snakemake.output[0]} "
"{log}"
)