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Commit 4969bdc2 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Reduce simple test data size and specify chemistry version

parent e90f8334
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3 merge requests!29Develop,!28Develop,!27Resolve "Develop CI"
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.gitlab-ci.yml
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......@@ -5,7 +5,7 @@ before_script:
- mkdir test_data/hu.v2s1r1k
- mkdir test_data/mu.v2s2r10k
- mkdir test_data/hu.v3s2r10k
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r1k/* test_data/hu.v2s1r1k/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
......@@ -22,18 +22,18 @@ astrocyte_check:
run_hu.cr3v2ref3.0.0:
stage: simple
script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
run_mu.cr2v2ref1.2.0:
stage: detailed
except:
- tags
script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'two' --version '2.1.1'
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'auto' --version '2.1.1'
run_hu.cr3v3ref3.0.0:
stage: detailed
except:
- tags
script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
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