PICARD COLLECTALIGNMENTSUMMARYMETRICS¶
Collect metrics on aligned reads with picard tools.
Example¶
This wrapper can be used in the following way:
rule alignment_summary:
input:
ref="genome.fasta",
bam="mapped/{sample}.bam",
output:
"stats/{sample}.summary.txt",
log:
"logs/picard/alignment-summary/{sample}.log",
params:
# optional parameters (e.g. relax checks as below)
extra="--VALIDATION_STRINGENCY LENIENT --METRIC_ACCUMULATION_LEVEL null --METRIC_ACCUMULATION_LEVEL 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:
"v1.19.1/bio/picard/collectalignmentsummarymetrics"
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#CollectAlignmentSummaryMetrics
Software dependencies¶
picard=2.27.4
snakemake-wrapper-utils=0.5.0
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell()
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"picard CollectAlignmentSummaryMetrics"
" {java_opts} {extra}"
" --INPUT {snakemake.input.bam}"
" --REFERENCE_SEQUENCE {snakemake.input.ref}"
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output[0]}"
" {log}"
)