PICARD COLLECTALIGNMENTSUMMARYMETRICS¶
Collect metrics on aligned reads with picard tools.
URL:
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)
"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:
"0.80.1/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.
Software dependencies¶
picard==2.22.1
snakemake-wrapper-utils==0.1.3
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell()
extra = snakemake.params
java_opts = get_java_opts(snakemake)
shell(
"picard CollectAlignmentSummaryMetrics {java_opts} {extra} "
"INPUT={snakemake.input.bam} OUTPUT={snakemake.output[0]} "
"REFERENCE_SEQUENCE={snakemake.input.ref} {log}"
)