SAMTOOLS SORT¶
Sort bam file with samtools. For more information see SAMtools documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule samtools_sort:
input:
"mapped/{sample}.bam"
output:
"mapped/{sample}.sorted.bam"
params:
extra = "-m 4G",
tmp_dir = "/tmp/"
threads: # Samtools takes additional threads through its option -@
8 # This value - 1 will be sent to -@.
wrapper:
"0.80.1/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.
Software dependencies¶
samtools==1.10
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
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
out_name, out_ext = os.path.splitext(snakemake.output[0])
tmp_dir = snakemake.params.get("tmp_dir", "")
if tmp_dir:
prefix = os.path.join(tmp_dir, os.path.basename(out_name))
else:
prefix = out_name
# 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 {extra} {threads} -o {snakemake.output[0]} "
"-T {prefix} {snakemake.input[0]} "
"{log}"
)