SAMTOOLS SORT
Sort bam file with samtools.
URL: http://www.htslib.org/doc/samtools-sort.html
Example
This wrapper can be used in the following way:
rule samtools_sort:
input:
"mapped/{sample}.bam",
output:
"mapped/{sample}.sorted.bam",
log:
"logs/{sample}.log",
params:
extra="-m 4G",
threads: 8
wrapper:
"v5.8.0-3-g915ba34/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=1.21
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
SAM/BAM/CRAM file
Output:
SAM/BAM/CRAM file
SAM/BAM/CRAM index file (optional)
Params
extra
: additional program arguments (not -@/–threads, –write-index, -m, -o or -O/–output-fmt).
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
import tempfile
from pathlib import Path
from snakemake.shell import shell
from snakemake_wrapper_utils.snakemake import get_mem
from snakemake_wrapper_utils.samtools import get_samtools_opts
samtools_opts = get_samtools_opts(snakemake)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
# `-m`: Approximately the maximum required memory per thread [...]
# samtools sort can use more memory than specified (e.g. https://github.com/samtools/samtools/issues/831)
mem_overhead_factor = snakemake.params.get("mem_overhead_factor", 0.1)
mem_per_thread_mb = int(
get_mem(snakemake) / snakemake.threads * (1.0 - mem_overhead_factor)
)
with tempfile.TemporaryDirectory() as tmpdir:
tmp_prefix = Path(tmpdir) / "samtools_sort"
shell(
"samtools sort {samtools_opts} -m {mem_per_thread_mb}M {extra} -T {tmp_prefix} {snakemake.input[0]} {log}"
)