PICARD REVERTSAM¶
Reverts SAM or BAM files to a previous state. .
Software dependencies¶
- picard ==2.18.16
Example¶
This wrapper can be used in the following way:
rule revert_bam:
input:
"mapped/{sample}.bam"
output:
"revert/{sample}.bam"
log:
"logs/picard/revert_sam/{sample}.log"
params:
extra="SANITIZE=true" # optional: Extra arguments for picard.
wrapper:
"0.34.0/bio/picard/revertsam"
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¶
- Patrik Smeds
Code¶
"""Snakemake wrapper for picard RevertSam."""
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
'picard'
' RevertSam'
' {extra}'
' INPUT={snakemake.input[0]}'
' OUTPUT={snakemake.output[0]}'
' {log}')