Newer
Older
#!/usr/bin/env python3
# -----------------------------------------------------------------------------
# Author : Maria Katsantoni, Maciek Bak
# Company: Mihaela Zavolan, Biozentrum, Basel
# This script is part of the Zavolan lab ZARP pipeline.
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
# In this script the config file used by multiqc
# (https://multiqc.info) is created.
# -----------------------------------------------------------------------------
import sys
from argparse import ArgumentParser, RawTextHelpFormatter
import os
def main():
""" Create config file for multiqc"""
__doc__ = "Create config file for multiqc"
parser = ArgumentParser(description=__doc__,
formatter_class=RawTextHelpFormatter)
parser.add_argument("--config",
help="Output file destination for config",
required=True,
metavar="FILE",)
parser.add_argument("--intro-text",
dest="intro_text",
help="short description at the top of report",
metavar="STR")
parser.add_argument("--custom-logo",
dest="custom_logo",
default='None',
help="Logo path",
metavar="FILE")
parser.add_argument("--url",
help="Url of the lab",
metavar="STR")
parser.add_argument("--author-name",
dest="author_name",
default='None',
help="Name of person running this analysis",
metavar="STR")
parser.add_argument("--author-email",
dest="author_email",
default='None',
help="email of person running this analysis",
metavar="STR")
try:
options = parser.parse_args()
except(Exception):
parser.print_help()
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
subtitle = "RNA-Seq processing pipeline developed by Zavolan Lab"
project_type = "Snakemake workflow"
analysis_type = "RNA-seq"
intro_text = options.intro_text
custom_logo = options.custom_logo
url = options.url
author_name = options.author_name
author_email = options.author_email
config_string = f"""---
title: "{title}"
subtitle: "{subtitle}"
intro_text: "{intro_text}"
custom_logo: "{custom_logo}"
custom_logo_url: "{url}"
custom_logo_title: "{logo_title}"
report_header_info:
- Project Type: "{project_type}"
- Analysis Type: "{analysis_type}"
- Analysis Author: "{author_name}"
- Contact E-mail: "{author_email}"
- fastqc:
path_filters:
- "*/*/fastqc/*/*"
- cutadapt:
name: "Cutadapt: adapter removal"
path_filters:
- "*/*/*remove_adapters_cutadapt*.stdout.log"
- cutadapt:
name: "Cutadapt: polyA tails removal"
path_filters:
- "*/*/*remove_polya_cutadapt*.stdout.log"
- star:
path_filters:
- "*/*/map_genome/*"
- "*/*/ALFA/*/*ALFA_feature_counts.tsv"
- "*/*/TIN/TIN_score.tsv"
- salmon:
path_filters:
- "*/*/*.salmon.*/*"
- kallisto:
path_filters:
- "*/*/*genome_quantification_kallisto*.stderr.log"
- zpca:
name: "zpca: salmon | gene expression"
path_filters:
- "*/zpca/pca_salmon_genes/*"
- zpca:
name: "zpca: salmon | transcript expression"
path_filters:
- "*/zpca/pca_salmon_transcripts/*"
- zpca:
name: "zpca: kallisto | gene expression"
path_filters:
- "*/zpca/pca_kallisto_genes/*"
- zpca:
name: "zpca: kallisto | transcript expression"
path_filters:
- "*/zpca/pca_kallisto_transcripts/*"
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
fn_clean_exts:
- '.fq1'
- '.gz'
- '.stdout'
- '.log'
- '.stderr'
- '.fastq'
- '.bam'
- '.bai'
- '.pe'
- '.se'
- '.pseudo'
- '.salmon'
- '.sam'
..."""
with open(options.config, "w") as config:
config.write(config_string)
return
if __name__ == '__main__':
try:
main()
except KeyboardInterrupt:
sys.stderr.write("User interrupt!")
sys.exit(1)