GATK CLEANSAM¶
Run gatk CleanSam
URL:
Example¶
This wrapper can be used in the following way:
rule gatk_clean_sam:
input:
bam="{sample}.bam"
output:
clean="{sample}.clean.bam"
log:
"logs/{sample}.log"
params:
extra="",
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"0.80.0/bio/gatk/cleansam"
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¶
gatk4==4.2.0.0
snakemake-wrapper-utils==0.1.3
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The extra param allows for additional program arguments.
- For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/360056970832-CleanSam-Picard-
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' CleanSam --INPUT {snakemake.input.bam} "
"{extra} --OUTPUT {snakemake.output.clean} {log}"
)