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Commit d4074018 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Add Nextflow Tower to CI

parent 15542ebf
1 merge request!63Develop
Pipeline #5001 failed with stages
in 47 seconds
...@@ -2,7 +2,7 @@ before_script: ...@@ -2,7 +2,7 @@ before_script:
- module load astrocyte - module load astrocyte
- module load python/3.6.1-2-anaconda - module load python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load nextflow/0.31.1_Ignite - module load nextflow/19.09.0
- mkdir test_data/hu.v3s1r500 - mkdir test_data/hu.v3s1r500
- mkdir test_data/mu.v3s1r500 - mkdir test_data/mu.v3s1r500
- mkdir test_data/hu.v3s2r10k - mkdir test_data/hu.v3s2r10k
...@@ -40,7 +40,7 @@ simple_1: ...@@ -40,7 +40,7 @@ simple_1:
- develop - develop
- master - master
script: script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0' - nextflow run workflow/main.nf --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
- pytest -m count310 - pytest -m count310
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -65,7 +65,7 @@ simple_2: ...@@ -65,7 +65,7 @@ simple_2:
- master - master
- tags - tags
script: script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0' - nextflow run workflow/main.nf --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
- pytest -m count310 - pytest -m count310
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -89,7 +89,7 @@ detailed_1: ...@@ -89,7 +89,7 @@ detailed_1:
refs: refs:
- tags - tags
script: script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0' - nextflow run workflow/main.nf --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0' -with-tower
- pytest -m count310 - pytest -m count310
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -114,7 +114,7 @@ detailed_2: ...@@ -114,7 +114,7 @@ detailed_2:
refs: refs:
- tags - tags
script: script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' - nextflow run workflow/main.nf --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' -with-tower
- pytest -m count302 - pytest -m count302
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -138,7 +138,7 @@ detailed_3: ...@@ -138,7 +138,7 @@ detailed_3:
refs: refs:
- tags - tags
script: script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1' - nextflow run workflow/main.nf --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1' -with-tower
- pytest -m count301 - pytest -m count301
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -162,7 +162,7 @@ detailed_4: ...@@ -162,7 +162,7 @@ detailed_4:
refs: refs:
- tags - tags
script: script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' - nextflow run workflow/main.nf --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' -with-tower
- pytest -m count211 - pytest -m count211
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
......
# v1.3.0 (in development)
**User Facing**
**Background**
* Add Nextflow Tower integration into CI (GHH's profile)
*Known Bugs*
# v1.2.0 # v1.2.0
**User Facing** **User Facing**
* Add Cellranger Version 3.1.0 * Add Cellranger Version 3.1.0
......
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