SAMTOOLS SORT¶
Sort bam file with samtools.
Software dependencies¶
- samtools ==1.9
Example¶
This wrapper can be used in the following way:
rule samtools_sort:
input:
"mapped/{sample}.bam"
output:
"mapped/{sample}.sorted.bam"
params:
"-m 4G"
threads: # Samtools takes additional threads through its option -@
8 # This value - 1 will be sent to -@.
wrapper:
"0.45.1/bio/samtools/sort"
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.
Notes¶
- Samtools -@/–threads takes one integer as input. This is the number of additional threads and not raw threads.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
import os
from snakemake.shell import shell
prefix = os.path.splitext(snakemake.output[0])[0]
# Samtools takes additional threads through its option -@
# One thread for samtools
# Other threads are *additional* threads passed to the argument -@
threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)
shell(
"samtools sort {snakemake.params} {threads} -o {snakemake.output[0]} "
"-T {prefix} {snakemake.input[0]}"
)