Commit 09166b21 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

gitlab update

parent 21d8e052
Pipeline #1662 failed with stage
in 1 minute
......@@ -2,16 +2,12 @@
# Brandi L. Cantarel - 2017
variables:
RUNDIR: "/project/BICF/BICF_Core/shared/astrocyte_test_ci/rnaseq_test"
TEST_BRANCH: "master"
GIT_SUBMODULE_STATEGY: recursive
before_script:
- module load nextflow/0.27.6
- mkdir -p "${RUNDIR}"
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/* ${RUNDIR}/test_data/
- echo $RUNDIR
- ls -l ${RUNDIR}/test_data/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq test_data
stages:
- integration
......@@ -19,17 +15,13 @@ stages:
test_human:
stage: integration
script:
- nextflow run workflow/main.nf --design ${RUNDIR}/test_data/design.rnaseq.txt --input ${RUNDIR}/test_data --output ${RUNDIR}/human_output
- nextflow run workflow/main.nf --design test_data/design.rnaseq.txt --input test_data --output human_output
artifacts:
paths:
- ${RUNDIR}
expire_in: 2 days
test_mouse:
stage: integration
script:
- nextflow run workflow/main.nf --input ${RUNDIR}/test_data --design ${RUNDIR}/test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output ${RUNDIR}/mouse_output
- 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
artifacts:
paths:
- ${RUNDIR}
expire_in: 2 days
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