picard picard collectalignmentsummarymetrics

picard collectalignmentsummarymetrics

Version:
2.22.1
Identifier: TL_e24fa5_2c.ea
Tool
1__author__ = "Johannes Köster"
2__copyright__ = "Copyright 2016, Johannes Köster"
3__email__ = "johannes.koester@protonmail.com"
4__license__ = "MIT"
5
6
7from snakemake.shell import shell
8from snakemake_wrapper_utils.java import get_java_opts
9
10log = snakemake.log_fmt_shell()
11
12extra = snakemake.params
13java_opts = get_java_opts(snakemake)
14
15shell(
16    "picard CollectAlignmentSummaryMetrics {java_opts} {extra} "
17    "INPUT={snakemake.input.bam} OUTPUT={snakemake.output[0]} "
18    "REFERENCE_SEQUENCE={snakemake.input.ref} {log}"
19)
20