diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index bde45e13872f96519e3d9c36f8009d680f675113..732c04c86db9bfc4983d9002855744f97d549df7 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -35,7 +35,7 @@ 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: @@ -45,7 +45,7 @@ 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: @@ -55,7 +55,7 @@ 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: @@ -65,7 +65,7 @@ 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 @@ -74,7 +74,7 @@ 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 @@ -83,5 +83,5 @@ 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