lofreq call
Version:1.6
1.6
Identifier: TL_a7703a_53.43
Tool
1__author__ = "Patrik Smeds"
2__copyright__ = "Copyright 2018, Patrik Smeds"
3__email__ = "patrik.smeds@gmail.com"
4__license__ = "MIT"
5
6
7import os
8from snakemake.shell import shell
9
10log = snakemake.log_fmt_shell(stdout=False, stderr=True)
11extra = snakemake.params.get("extra", "")
12ref = snakemake.params.get("ref", None)
13
14if ref is None:
15 raise ValueError("A reference must be provided")
16
17bam_input = snakemake.input.bam
18bai_input = snakemake.input.bai
19
20if bam_input is None:
21 raise ValueError("Missing bam input file!")
22
23if bai_input is None:
24 raise ValueError("Missing bai input file!")
25
26output_file = snakemake.output[0]
27
28if output_file is None:
29 raise ValueError("Missing output file")
30elif not len(snakemake.output) == 1:
31 raise ValueError("Only expecting one output file: " + str(output_file) + "!")
32
33shell(
34 "lofreq call-parallel "
35 " --pp-threads {snakemake.threads}"
36 " -f {ref}"
37 " {bam_input}"
38 " -o {output_file}"
39 " {extra}"
40 " {log}"
41)
42