diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 85ce1e09ca0c0d41b3665820f5526138a4779e43..2eaaa76056d8d6a0949aa8cadd4262a946fd8579 100755 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -40,7 +40,7 @@ simple_1: - develop - master script: - - nextflow -bg run workflow/main.nf -config 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' + - nextflow -q 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' artifacts: name: "$CI_JOB_NAME" when: always @@ -64,7 +64,7 @@ simple_2: - master - tags script: - - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' + - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' artifacts: name: "$CI_JOB_NAME" when: always @@ -87,7 +87,7 @@ detailed_1: refs: - tags script: - - nextflow -bg run workflow/main.nf -config 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' + - nextflow -q 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' artifacts: name: "$CI_JOB_NAME" when: always @@ -111,7 +111,7 @@ detailed_2: refs: - tags script: - - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' + - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' artifacts: name: "$CI_JOB_NAME" when: always @@ -134,7 +134,7 @@ detailed_3: refs: - tags script: - - nextflow -bg run workflow/main.nf -config 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' + - nextflow -q 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' artifacts: name: "$CI_JOB_NAME" when: always @@ -157,7 +157,7 @@ detailed_4: refs: - tags script: - - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' + - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' artifacts: name: "$CI_JOB_NAME" when: always diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config index 65b98626f7fe547a1de9221f866c0b1fd65f45f4..d6c70870870bb37af1246d39d0456efe54f07ed0 100644 --- a/workflow/conf/biohpc_cluster.config +++ b/workflow/conf/biohpc_cluster.config @@ -5,7 +5,7 @@ process { withLabel: checkDesignFile { module = ['python/3.6.1-2-anaconda'] - executor = 'local' + queue = '32GB' } withLabel: count211 { module = ['cellranger/2.1.1'] @@ -25,11 +25,11 @@ process { } withLabel: versions { module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7'] - executor = 'local' + queue = '32GB' } withLabel: multiqc { module = ['multiqc/1.7'] - executor = 'local' + queue = '32GB' } }