SAMBAMBA FLAGSTAT¶
Outputs some statistics drawn from read flags. See details `here https://lomereiter.github.io/sambamba/docs/sambamba-flagstat.html`_
URL:
Example¶
This wrapper can be used in the following way:
rule sambamba_flagstat:
input:
"mapped/{sample}.bam"
output:
"mapped/{sample}.stats.txt"
params:
extra="" # optional parameters
log:
"logs/sambamba-flagstat/{sample}.log"
threads: 1
wrapper:
"0.85.0/bio/sambamba/flagstat"
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=False, stderr=True)
shell(
"sambamba flagstat {snakemake.params.extra} -t {snakemake.threads} "
"{snakemake.input[0]} > {snakemake.output[0]} "
"{log}"
)