From 09166b216229706c95ebe1829ed619c3fc5c70b5 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 15 Mar 2018 16:53:06 -0500
Subject: [PATCH] gitlab update
---
.gitlab-ci.yml | 14 +++-----------
1 file changed, 3 insertions(+), 11 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bfc71b3..e1b45b5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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
--
GitLab