PICARD MERGESAMFILES¶
Merge sam/bam files using picard tools.
URL:
Example¶
This wrapper can be used in the following way:
rule merge_bams:
input:
expand("mapped/{sample}.bam", sample=["a", "b"])
output:
"merged.bam"
log:
"logs/picard_mergesamfiles.log"
params:
"VALIDATION_STRINGENCY=LENIENT"
# 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:
"0.80.1/bio/picard/mergesamfiles"
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¶
- Julian de Ruiter
Code¶
"""Snakemake wrapper for picard MergeSamFiles."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__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)
inputs = " ".join("INPUT={}".format(in_) for in_ in snakemake.input)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"picard"
" MergeSamFiles"
" {java_opts} {extra}"
" {inputs}"
" OUTPUT={snakemake.output[0]}"
" {log}"
)