Commit 044e65cc authored by Jeremy Mathews's avatar 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
...@@ -6,8 +6,10 @@ before_script: ...@@ -6,8 +6,10 @@ before_script:
- module load singularity/3.5.3 - module load singularity/3.5.3
- mkdir -p test_data/simple1 - mkdir -p test_data/simple1
- mkdir -p test_data/simple2 - 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/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/simple2/* test_data/simple2/
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple3/* test_data/simple3/
stages: stages:
- astrocyte - astrocyte
...@@ -27,7 +29,7 @@ astrocyte_check: ...@@ -27,7 +29,7 @@ astrocyte_check:
simple_1FC: simple_1FC:
stage: simple stage: simple
script: 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 ##- pytest -m simple1
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -44,7 +46,7 @@ simple_1FC: ...@@ -44,7 +46,7 @@ simple_1FC:
simple_2FC: simple_2FC:
stage: simple stage: simple
script: 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 ##- pytest -m simple2
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -57,3 +59,20 @@ simple_2FC: ...@@ -57,3 +59,20 @@ simple_2FC:
max: 0 max: 0
when: when:
- always - 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
...@@ -12,13 +12,17 @@ from io import StringIO ...@@ -12,13 +12,17 @@ from io import StringIO
import os import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/mkfastq/' '/../output/'
@pytest.mark.simple1 @pytest.mark.simple1
def test_simple1_mkfastq(): 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 @pytest.mark.simple2
def test_simple2_mkfastq(): 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, 'mkfastq', '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')) assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0-2', 'outs'))
\ No newline at end of file
@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'))
...@@ -20,4 +20,8 @@ def test_simple1_multiqc(): ...@@ -20,4 +20,8 @@ def test_simple1_multiqc():
@pytest.mark.simple2 @pytest.mark.simple2
def test_simple2_multiqc(): def test_simple2_multiqc():
assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html')) assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
\ No newline at end of file
@pytest.mark.simple3
def test_simple3_multiqc():
assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
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