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BICF
Astrocyte
chipseq_analysis
Commits
c045ad59
Commit
c045ad59
authored
Feb 24, 2020
by
Venkat Malladi
Browse files
Merge branch 'master' into '67-python_version'
# Conflicts: # CHANGELOG.md
parents
ded90cf9
876e2cc6
Pipeline
#6100
failed with stages
in 606 minutes and 55 seconds
Changes
3
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CHANGELOG.md
View file @
c045ad59
...
...
@@ -15,6 +15,8 @@ All notable changes to this project will be documented in this file.
-
Fix xcor to increase file size for --random-source
-
Fix skip diff test for paired-end data
-
Fix python version for MultiQC report
-
Fix references to display in Multiqc report
## [publish_1.0.6 ] - 2019-05-31
### Added
...
...
workflow/main.nf
View file @
c045ad59
...
...
@@ -654,10 +654,10 @@ process multiqcReport {
"""
echo $workflow.nextflow.version > version_nextflow.txt
singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc
.sif
multiqc --version > version_multiqc.txt
singularity exec /project/shared/bicf_workflow_ref/singularity_images/
bicf-
multiqc
-2.0.0.img
multiqc --version > version_multiqc.txt
python --version &> version_python.txt
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
python3 $baseDir/scripts/generate_versions.py -o software_versions
singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc
.sif
multiqc -c $multiqc .
singularity exec /project/shared/bicf_workflow_ref/singularity_images/
bicf-
multiqc
-2.0.0.img
multiqc -c $multiqc .
"""
}
workflow/tests/test_generate_software_references.py
View file @
c045ad59
...
...
@@ -4,6 +4,7 @@ import pytest
import
os
import
utils
import
yaml
from
bs4
import
BeautifulSoup
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/multiqcReport/'
...
...
@@ -21,3 +22,14 @@ def test_software_references_output():
data_loaded
=
yaml
.
load
(
stream
)
assert
len
(
data_loaded
[
'data'
].
split
(
'<ul>'
))
==
19
@
pytest
.
mark
.
singleend
def
test_software_references_html
():
multiqc_report
=
os
.
path
.
join
(
test_output_path
,
'multiqc_report.html'
)
html_file
=
open
(
multiqc_report
,
'r'
)
source_code
=
html_file
.
read
()
multiqc_html
=
BeautifulSoup
(
source_code
,
'html.parser'
)
references
=
multiqc_html
.
find
(
id
=
"mqc-module-section-Software_References"
)
assert
references
is
not
None
assert
len
(
references
.
find_all
(
'ul'
))
==
18
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