Commit 87256997 authored by Brandi Cantarel's avatar Brandi Cantarel

gitlab update

parent 1d13db11
Pipeline #1664 failed with stage
in 34 seconds
......@@ -7,6 +7,7 @@ variables:
before_script:
- module load nextflow/0.27.6
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq test_data
stages:
- integration
......@@ -14,13 +15,13 @@ stages:
test_human:
stage: integration
script:
- nextflow run workflow/main.nf --design test_data/design.rnaseq.txt --input test_data --output human_output
- nextflow run workflow/main.nf --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output
artifacts:
expire_in: 2 days
test_mouse:
stage: integration
script:
- nextflow run workflow/main.nf --input test_data --design test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output mouse_output
- nextflow run workflow/main.nf --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output mouse_output
artifacts:
expire_in: 2 days
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