diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c5a0ec4293a731f76b0f06c34a5e8bb8b965cc6c..5a9c93c0d747b0218ec1407002d7d376e34a2421 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -30,7 +30,7 @@ single_end_mouse: only: - master script: - - nextflow run workflow/main.nf --astrocyte true + - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true - pytest -m singleend paired_end_human: @@ -40,7 +40,7 @@ paired_end_human: except: - master script: - - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false + - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false - pytest -m pairedend single_end_single_control: @@ -50,7 +50,7 @@ single_end_single_control: except: - master script: - - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false + - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false - pytest -m singlecontrol single_end_diff: @@ -60,7 +60,7 @@ single_end_diff: except: - master script: - - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false + - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false - pytest -m singleend - pytest -m singlediff @@ -69,7 +69,7 @@ paired_end_diff: - master stage: multiple script: - - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false + - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false - pytest -m pairedend - pytest -m paireddiff @@ -78,5 +78,5 @@ single_end_skip: only: - master script: - - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false + - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false - pytest -m singleskip_true