PICARD ADDORREPLACEREADGROUPS¶
Add or replace read groups with picard tools.
URL:
Example¶
This wrapper can be used in the following way:
rule replace_rg:
input:
"mapped/{sample}.bam"
output:
"fixed-rg/{sample}.bam"
log:
"logs/picard/replace_rg/{sample}.log"
params:
"RGLB=lib1 RGPL=illumina RGPU={sample} RGSM={sample}"
# optional specification of memory usage of the JVM that snakemake will respect with global
# resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
# and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=1024
wrapper:
"0.85.0/bio/picard/addorreplacereadgroups"
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¶
picard==2.22.1
snakemake-wrapper-utils==0.1.3
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params
java_opts = get_java_opts(snakemake)
shell(
"picard AddOrReplaceReadGroups {java_opts} {extra} "
"I={snakemake.input} O={snakemake.output} &> {snakemake.log}"
)