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chipseq_analysis
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BICF
Astrocyte
chipseq_analysis
Commits
5055cccb
Commit
5055cccb
authored
5 years ago
by
Venkat Malladi
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Test data for single control single replicate.
parent
ca3e17e3
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1 merge request
!63
Resolve "Single Rep Pool and Pseudo"
Pipeline
#5971
canceled with stages
in 6 minutes and 5 seconds
Changes
3
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1
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3 changed files
.gitlab-ci.yml
+2
-2
2 additions, 2 deletions
.gitlab-ci.yml
test_data/design_single_contol_SE.txt
+0
-1
0 additions, 1 deletion
test_data/design_single_contol_SE.txt
workflow/tests/test_overlap_peaks.py
+6
-0
6 additions, 0 deletions
workflow/tests/test_overlap_peaks.py
with
8 additions
and
3 deletions
.gitlab-ci.yml
+
2
−
2
View file @
5055cccb
...
...
@@ -14,7 +14,6 @@ stages:
user_configuration
:
stage
:
unit
script
:
-
pytest -m unit
-
pytest -m unit --cov=./workflow/scripts
astrocyte
:
...
...
@@ -51,7 +50,8 @@ single_end_single_control:
-
master
script
:
-
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd
false
--astrocyte
false
-
pytest -m singlecontrol
single_end_diff
:
stage
:
multiple
only
:
...
...
This diff is collapsed.
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test_data/design_single_contol_SE.txt
+
0
−
1
View file @
5055cccb
sample_id experiment_id biosample factor treatment replicate control_id fastq_read1
ENCLB497XZB ENCSR000DXB Panc1 H3K4me3 None 1 ENCLB304SBJ ENCFF001GBW.fastq.gz
ENCLB414AAH ENCSR000DXB Panc1 H3K4me3 None 2 ENCLB304SBJ ENCFF001GBV.fastq.gz
ENCLB304SBJ ENCSR000DXC Panc1 Control None 1 ENCLB304SBJ ENCFF001HWJ.fastq.gz
This diff is collapsed.
Click to expand it.
workflow/tests/test_overlap_peaks.py
+
6
−
0
View file @
5055cccb
...
...
@@ -45,3 +45,9 @@ def test_overlap_peaks_pairedend():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'
ENCSR729LGA.rejected.narrowPeak
'
))
peak_file
=
test_output_path
+
'
ENCSR729LGA.replicated.narrowPeak
'
assert
utils
.
count_lines
(
peak_file
)
>=
25657
@pytest.mark.singlecontrol
def
test_overlap_peaks_singlecontrol
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'
ENCSR000DXB.rejected.narrowPeak
'
))
peak_file
=
test_output_path
+
'
ENCSR000DXB.replicated.narrowPeak
'
assert
utils
.
count_lines
(
peak_file
)
>=
35097
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