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chipseq_analysis
Commit 92ea443a authored by Venkat Malladi's avatar Venkat Malladi
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Add Nextflow opts.

parent e09a8b62
Pipeline #6405 failed with stages
          in 22 minutes and 19 seconds
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          Showing with 6 additions and 6 deletions
          .gitlab-ci.yml
          View file @ 92ea443a
          ......@@ -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
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