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chipseq_analysis
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Astrocyte
Workflows
BICF
chipseq_analysis
Commits
763ac90a
Commit
763ac90a
authored
5 years ago
by
Venkat Malladi
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Fix config for references.
parent
15122e72
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workflow/conf/multiqc_config.yaml
+36
-0
36 additions, 0 deletions
workflow/conf/multiqc_config.yaml
workflow/main.nf
+2
-2
2 additions, 2 deletions
workflow/main.nf
workflow/scripts/generate_references.py
+7
-6
7 additions, 6 deletions
workflow/scripts/generate_references.py
with
45 additions
and
8 deletions
workflow/conf/multiqc_config.yaml
0 → 100644
+
36
−
0
View file @
763ac90a
# Title to use for the report.
title
:
BICF ChIP-seq Analysis Report
report_comment
:
>
This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/" target="_blank">BICF/chipseq_analysis</a>
pipeline.
report_section_order
:
software_versions
:
order
:
-1000
report_section_order
:
software_references
:
order
:
-1000
extra_fn_clean_exts
:
-
'
_R1'
-
'
_R2'
-
'
pbc.qc'
fn_ignore_files
:
-
'
*dedup.flagstat.qc'
custom_data
:
library_complexity
:
file_format
:
'
tsv'
id
:
'
library_complexity'
contents
:
'
TotalReadPairs
DistinctReadPairs
OneReadPair
TwoReadPairs
NRF
PBC1
PBC2'
section_name
:
'
Library
complexity'
plot_type
:
'
generalstats'
sp
:
phantompeakqualtools/out
:
fn
:
'
*cc.qc'
library_complexity
:
fn
:
'
*pbc.qc'
This diff is collapsed.
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workflow/main.nf
+
2
−
2
View file @
763ac90a
...
...
@@ -505,8 +505,8 @@ process softwareReport {
output:
file('
*
_mqc.yaml') into softwareVersions
file('
*
_mqc.
txt
') into softwareReferences
file('
software_versions
_mqc.yaml') into softwareVersions
file('
software_references
_mqc.
yaml
') into softwareReferences
script:
"""
...
...
This diff is collapsed.
Click to expand it.
workflow/scripts/generate_references.py
+
7
−
6
View file @
763ac90a
...
...
@@ -44,20 +44,21 @@ def main():
reference
=
args
.
reference
output
=
args
.
output
out_filename
=
output
+
'
_mqc.
txt
'
out_filename
=
output
+
'
_mqc.
yaml
'
# Header for HTML
print
(
'''
# id:
'
References
'
# section_name:
'
References
'
# description:
'
This section describes references for the tools used.
'
# plot_type:
'
html
'
id:
'
Software References
'
section_name:
'
Software References
'
description:
'
This section describes references for the tools used.
'
plot_type:
'
html
'
data: |
'''
,
file
=
open
(
out_filename
,
"
w
"
)
)
# Turn Markdown into HTML
references_html
=
'
bash -c
"
pandoc
{}
>> {}
"'
references_html
=
'
bash -c
"
pandoc
-p {} | sed
\'
s/^/ /
\'
>> {}
"'
references_html
=
references_html
.
format
(
reference
,
out_filename
)
subprocess
.
check_call
(
shlex
.
split
(
references_html
))
...
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