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Commit 62642c4d authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Add nexflow.config to ci run

parent 2ebf343e
2 merge requests!63Develop,!60Resolve "Add 3':5' param"
Pipeline #6532 passed with stages
in 12 seconds
...@@ -40,7 +40,7 @@ simple_1: ...@@ -40,7 +40,7 @@ simple_1:
- develop - develop
- master - master
script: script:
- nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -64,7 +64,7 @@ simple_2: ...@@ -64,7 +64,7 @@ simple_2:
- master - master
- tags - tags
script: script:
- nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -87,7 +87,7 @@ detailed_1: ...@@ -87,7 +87,7 @@ detailed_1:
refs: refs:
- tags - tags
script: script:
- nextflow -bg run workflow/main.nf -profile biohpc,cluster --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' - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --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'
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -111,7 +111,7 @@ detailed_2: ...@@ -111,7 +111,7 @@ detailed_2:
refs: refs:
- tags - tags
script: script:
- nextflow -bg run workflow/main.nf -profile biohpc,cluster --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' - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --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'
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -134,7 +134,7 @@ detailed_3: ...@@ -134,7 +134,7 @@ detailed_3:
refs: refs:
- tags - tags
script: script:
- nextflow -bg run workflow/main.nf -profile biohpc,cluster --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' - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --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'
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -157,7 +157,7 @@ detailed_4: ...@@ -157,7 +157,7 @@ detailed_4:
refs: refs:
- tags - tags
script: script:
- nextflow -bg run workflow/main.nf -profile biohpc,cluster --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' - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --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'
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
......
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