From 87256997d9144531410a1ec171a6e74b29c18c3d Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 15 Mar 2018 17:01:24 -0500
Subject: [PATCH] gitlab update
---
.gitlab-ci.yml | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c25db03..49bd46f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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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