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cellranger_mkfastq
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BICF
Astrocyte
cellranger_mkfastq
Commits
8ebc05b9
Commit
8ebc05b9
authored
Jul 22, 2019
by
Jeremy Mathews
Browse files
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Plain Diff
restructre pytests
parent
6dd85b3e
Pipeline
#4460
passed with stages
in 2 minutes and 29 seconds
Changes
7
Pipelines
1
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Showing
7 changed files
with
49 additions
and
33 deletions
+49
-33
.gitlab-ci.yml
.gitlab-ci.yml
+2
-12
workflow/tests/test_check_design.py
workflow/tests/test_check_design.py
+7
-4
workflow/tests/test_fastqc.py
workflow/tests/test_fastqc.py
+9
-4
workflow/tests/test_mkfastq.py
workflow/tests/test_mkfastq.py
+9
-5
workflow/tests/test_multiqc.py
workflow/tests/test_multiqc.py
+6
-2
workflow/tests/test_untarBCL.py
workflow/tests/test_untarBCL.py
+9
-4
workflow/tests/test_versions.py
workflow/tests/test_versions.py
+7
-2
No files found.
.gitlab-ci.yml
View file @
8ebc05b9
...
...
@@ -29,12 +29,7 @@ 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 design
-
pytest -m untarBCL
-
pytest -m mkfastq
-
pytest -m fastqc
-
pytest -m versions
-
pytest -m multiqc
-
pytest -m simple1
artifacts
:
name
:
"
$CI_JOB_NAME"
when
:
always
...
...
@@ -50,12 +45,7 @@ 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 design
-
pytest -m untarBCL
-
pytest -m mkfastq
-
pytest -m fastqc
-
pytest -m versions
-
pytest -m multiqc
-
pytest -m simple2
artifacts
:
name
:
"
$CI_JOB_NAME"
when
:
always
...
...
workflow/tests/test_check_design.py
View file @
8ebc05b9
...
...
@@ -8,7 +8,10 @@ import os
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/misc/checkDesignFile/run/'
@
pytest
.
mark
.
design
def
test_design
():
design_file
=
os
.
path
.
join
(
test_output_path
,
'design.checked.csv'
)
assert
os
.
path
.
exists
(
design_file
)
@
pytest
.
mark
.
simple1
def
test_simple1_design
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'design.checked.csv'
))
@
pytest
.
mark
.
simple2
def
test_simple2_design
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'design.checked.csv'
))
workflow/tests/test_fastqc.py
View file @
8ebc05b9
...
...
@@ -6,8 +6,13 @@ from io import StringIO
import
os
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/misc/fastqc/run/
cellranger-tiny-bcl-1_2_0/
'
'/../output/misc/fastqc/run/'
@
pytest
.
mark
.
fastqc
def
test_fastqc
():
assert
os
.
path
.
exists
(
test_output_path
)
@
pytest
.
mark
.
simple1
def
test_simple1_fastqc
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0'
))
@
pytest
.
mark
.
simple2
def
test_simple2_fastqc
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0-1'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0-2'
))
workflow/tests/test_mkfastq.py
View file @
8ebc05b9
...
...
@@ -4,11 +4,15 @@ import pytest
import
pandas
as
pd
from
io
import
StringIO
import
os
import
glob
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/mkfastq/
cellranger-tiny-bcl-1_2_0/outs/
'
'/../output/mkfastq/'
@
pytest
.
mark
.
mkfastq
def
test_mkfastq
():
assert
os
.
path
.
exists
(
test_output_path
)
@
pytest
.
mark
.
simple1
def
test_simple1_mkfastq
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0'
,
'outs'
))
@
pytest
.
mark
.
simple2
def
test_simple2_mkfastq
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0-1'
,
'outs'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0-2'
,
'outs'
))
workflow/tests/test_multiqc.py
View file @
8ebc05b9
...
...
@@ -8,6 +8,10 @@ import os
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/multiqc/run/'
@
pytest
.
mark
.
multiqc
def
test_multiqc
():
@
pytest
.
mark
.
simple1
def
test_simple1_multiqc
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'multiqc_report.html'
))
@
pytest
.
mark
.
simple2
def
test_simple2_multiqc
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'multiqc_report.html'
))
workflow/tests/test_untarBCL.py
View file @
8ebc05b9
...
...
@@ -6,8 +6,13 @@ from io import StringIO
import
os
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/untarBCL/
cellranger-tiny-bcl-1_2_0/
'
'/../output/untarBCL/'
@
pytest
.
mark
.
untarBCL
def
test_untarBCL
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'RTAComplete.txt'
))
@
pytest
.
mark
.
simple1
def
test_simple1_untarBCL
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0'
,
'RTAComplete.txt'
))
@
pytest
.
mark
.
simple2
def
test_simple2_untarBCL
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0-1'
,
'RTAComplete.txt'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0-2'
,
'RTAComplete.txt'
))
workflow/tests/test_versions.py
View file @
8ebc05b9
...
...
@@ -8,7 +8,12 @@ import os
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/misc/versions/run/'
@
pytest
.
mark
.
versions
def
test_versions
():
@
pytest
.
mark
.
simple1
def
test_simple1_versions
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'versions_mqc.yaml'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'references_mqc.yaml'
))
@
pytest
.
mark
.
simple2
def
test_simple2_versions
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'versions_mqc.yaml'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'references_mqc.yaml'
))
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