picard picard collecthsmetrics

picard collecthsmetrics

Version:
2.22.1
Identifier: TL_e24fa5_19.ea
Tool
1"""Snakemake wrapper for picard CollectHSMetrics."""
2# Snakemake wrappers are provided by Truwl to teach the internal mechanics of Snakemake recipes. View https://github.com/snakemake/snakemake-wrappers to learn how to use wrappers.
3
4__author__ = "Julian de Ruiter"
5__copyright__ = "Copyright 2017, Julian de Ruiter"
6__email__ = "julianderuiter@gmail.com"
7__license__ = "MIT"
8
9
10from snakemake.shell import shell
11from snakemake_wrapper_utils.java import get_java_opts
12
13
14inputs = " ".join("INPUT={}".format(in_) for in_ in snakemake.input)
15extra = snakemake.params.get("extra", "")
16log = snakemake.log_fmt_shell(stdout=False, stderr=True)
17java_opts = get_java_opts(snakemake)
18
19shell(
20    "picard CollectHsMetrics"
21    " {java_opts} {extra}"
22    " INPUT={snakemake.input.bam}"
23    " OUTPUT={snakemake.output[0]}"
24    " REFERENCE_SEQUENCE={snakemake.input.reference}"
25    " BAIT_INTERVALS={snakemake.input.bait_intervals}"
26    " TARGET_INTERVALS={snakemake.input.target_intervals}"
27    " {log}"
28)
29