PICARD ADDORREPLACEREADGROUPS¶
Add or replace read groups with picard tools.
Software dependencies¶
- picard ==2.9.2
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}"
wrapper:
"0.33.0/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.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
shell("picard AddOrReplaceReadGroups {snakemake.params} I={snakemake.input} "
"O={snakemake.output} &> {snakemake.log}")