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cellranger_mkfastq
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BICF
Astrocyte
cellranger_mkfastq
Commits
6cef4fe6
Commit
6cef4fe6
authored
5 years ago
by
Jeremy Mathews
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Add pytest
parent
b1e7748e
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2 merge requests
!41
Develop
,
!40
Resolve "Add pytest to CI"
Pipeline
#4425
failed with stages
in 5 minutes and 36 seconds
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.gitlab-ci.yml
+3
-1
3 additions, 1 deletion
.gitlab-ci.yml
workflow/tests/test_fastqc.py
+14
-0
14 additions, 0 deletions
workflow/tests/test_fastqc.py
with
17 additions
and
1 deletion
.gitlab-ci.yml
+
3
−
1
View file @
6cef4fe6
...
...
@@ -28,6 +28,7 @@ simple_1FC:
-
tags
script
:
-
nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv"
-
pytest -m fastqc
artifacts
:
name
:
"
$CI_JOB_NAME"
when
:
always
...
...
@@ -43,6 +44,7 @@ simple_2FC:
stage
:
simple
script
:
-
nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
-
pytest -m fastqc
artifacts
:
name
:
"
$CI_JOB_NAME"
when
:
always
...
...
@@ -52,4 +54,4 @@ simple_2FC:
retry
:
max
:
2
when
:
-
always
\ No newline at end of file
-
always
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workflow/tests/test_fastqc.py
0 → 100644
+
14
−
0
View file @
6cef4fe6
#!/usr/bin/env python3
import
pytest
import
pandas
as
pd
from
io
import
StringIO
import
os
import
glob
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'
/../../test/mkfastq/
'
@pytest.mark.fastqc
def
test_fastqc_output
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
glob
.
glob
(
'
*.fastq.gz
'
,
recursive
=
True
)))
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