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BICF
Astrocyte
cellranger_mkfastq
Commits
044e65cc
Commit
044e65cc
authored
Nov 04, 2020
by
Jeremy Mathews
Browse files
add spaceranger to CI and add to testdata location on shared folder
parent
369238e8
Pipeline
#8288
passed with stages
in 6 minutes and 54 seconds
Changes
3
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
.gitlab-ci.yml
View file @
044e65cc
...
...
@@ -6,8 +6,10 @@ before_script:
-
module load singularity/3.5.3
-
mkdir -p test_data/simple1
-
mkdir -p test_data/simple2
-
mkdir -p test_data/simple3
-
ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/
-
ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple2/* test_data/simple2/
-
ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple3/* test_data/simple3/
stages
:
-
astrocyte
...
...
@@ -27,7 +29,7 @@ astrocyte_check:
simple_1FC
:
stage
:
simple
script
:
-
nextflow run workflow/main.nf -profile biohpc,cluster --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --ci
true
-
nextflow run workflow/main.nf -profile biohpc,cluster
--ranger "cellranger"
--bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --ci
true
##- pytest -m simple1
artifacts
:
name
:
"
$CI_JOB_NAME"
...
...
@@ -44,7 +46,7 @@ simple_1FC:
simple_2FC
:
stage
:
simple
script
:
-
nextflow run workflow/main.nf -profile biohpc,cluster --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci
true
-
nextflow run workflow/main.nf -profile biohpc,cluster
--ranger "cellranger"
--bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci
true
##- pytest -m simple2
artifacts
:
name
:
"
$CI_JOB_NAME"
...
...
@@ -57,3 +59,20 @@ simple_2FC:
max
:
0
when
:
-
always
simple_3FC
:
stage
:
simple
script
:
-
nextflow run workflow/main.nf -profile biohpc,cluster --ranger "spaceranger" --bcl "test_data/simple3/*.tar.gz" --designFile "test_data/simple3/spaceranger-tiny-bcl-simple-1.0.0.csv" --ci
true
##- pytest -m simple3
artifacts
:
name
:
"
$CI_JOB_NAME"
when
:
always
paths
:
-
.nextflow.log
-
workflow/output/multiqc/run/multiqc_report.html
expire_in
:
2 days
retry
:
max
:
0
when
:
-
always
workflow/tests/test_mkfastq.py
View file @
044e65cc
...
...
@@ -12,13 +12,17 @@ from io import StringIO
import
os
test_output_path
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
+
\
'/../output/
mkfastq/
'
'/../output/'
@
pytest
.
mark
.
simple1
def
test_simple1_mkfastq
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'cellranger-tiny-bcl-1_2_0'
,
'outs'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'mkfastq'
,
'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'
))
\ No newline at end of file
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'mkfastq'
,
'cellranger-tiny-bcl-1_2_0-1'
,
'outs'
))
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'mkfastq'
,
'cellranger-tiny-bcl-1_2_0-2'
,
'outs'
))
@
pytest
.
mark
.
simple3
def
test_simple3_mkfastq
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'spaceranger_mkfastq'
,
'mkfastq_spaceranger-tiny-bcl-1'
,
'outs'
))
workflow/tests/test_multiqc.py
View file @
044e65cc
...
...
@@ -20,4 +20,8 @@ def test_simple1_multiqc():
@
pytest
.
mark
.
simple2
def
test_simple2_multiqc
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'multiqc_report.html'
))
\ No newline at end of file
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'multiqc_report.html'
))
@
pytest
.
mark
.
simple3
def
test_simple3_multiqc
():
assert
os
.
path
.
exists
(
os
.
path
.
join
(
test_output_path
,
'multiqc_report.html'
))
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