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BICF
Astrocyte
cellranger_count
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!29
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Develop
develop
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10-count.features
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Merged
Gervaise Henry
requested to merge
develop
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10-count.features
6 years ago
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b69acc56
Merge branch '14-ci' into 'develop'
· b69acc56
Gervaise Henry
authored
6 years ago
Resolve "Develop CI" See merge request
!27
.gitlab-ci.yml
+
13
−
5
Options
@@ -2,30 +2,38 @@ before_script:
-
module load astrocyte
-
module load python/3.6.1-2-anaconda
-
module load nextflow/0.31.1_Ignite
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mkdir test_data/hu.v2s1r500
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mkdir test_data/mu.v2s2r10k
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mkdir test_data/hu.v3s2r10k
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ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
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ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
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ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
stages
:
-
astrocyte
-
run
-
simple
-
detailed
astrocyte_check
:
stage
:
astrocyte
script
:
-
astrocyte_cli check ../cellranger_count
run_hu.cr3v2ref3.0.0
:
stage
:
simple
script
:
-
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
:
run
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 't
w
o' --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 '
au
to' --version '2.1.1'
run_hu.cr3v3ref3.0.0
:
stage
:
run
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'