From 8747d42f29a8be90e78d4bec1e132f65d7443f5e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 15 Mar 2018 15:56:08 -0500
Subject: [PATCH] update gitlab-ci.yml
---
.gitlab-ci.yml | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5f50a87..ebba4fb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,13 +2,14 @@
# Brandi L. Cantarel - 2017
variables:
- CLEAN_REPO_PATH: "/project/BICF/BICF_Core/s166458/astrocyte_test/${CI_RUNNER_ID}"
+ RUNDIR: "/project/BICF/BICF_Core/shared/astrocyte_test_ci/rnaseq_test"
TEST_BRANCH: "master"
before_script:
- module load nextflow/0.27.6
- - mkdir -p "${CLEAN_REPO_PATH}"
- - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq ${CLEAN_REPO_PATH}/test_data
+ - mkdir -p "${RUNDIR}"
+ - echo $RUNDIR
+ - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq ${RUNDIR}/test_data
stages:
- integration
@@ -16,17 +17,17 @@ stages:
test_human:
stage: integration
script:
- - nextflow run workflow/main.nf --input test_data/ --design ${CLEAN_REPO_PATH}/test_data/design.rnaseq.txt --output ${CLEAN_REPO_PATH}/human_output
+ - nextflow run workflow/main.nf --design ${RUNDIR}/test_data/design.rnaseq.txt --input ${RUNDIR}/test_data --output ${RUNDIR}/human_output
artifacts:
paths:
- - ${CLEAN_REPO_PATH}
+ - ${RUNDIR}
expire_in: 2 days
test_mouse:
stage: integration
script:
- - nextflow run workflow/main.nf --input test_data/ --design ${CLEAN_REPO_PATH}/test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output ${CLEAN_REPO_PATH}/mouse_output
+ - 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
artifacts:
paths:
- - ${CLEAN_REPO_PATH}
+ - ${RUNDIR}
expire_in: 2 days
--
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