PICARD MERGESAMFILES¶
Merge sam/bam files using picard tools.
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:
extra="--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:
"v1.12.2/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.
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.
- –TMP_DIR is automatically set by resources.tmpdir
- For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#MergeSamFiles
Software dependencies¶
picard=2.27
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"
import tempfile
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)
inputs = " ".join("--INPUT {}".format(in_) for in_ in snakemake.input)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"picard MergeSamFiles"
" {java_opts} {extra}"
" {inputs}"
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output[0]}"
" {log}"
)