From 34d210b08a6419f88577fce04086c61f371983ad Mon Sep 17 00:00:00 2001
From: devagy74 <paula.iborradetoledo@unibas.ch>
Date: Thu, 26 Mar 2020 13:08:26 +0100
Subject: [PATCH] Fixing CI testing
---
.gitlab-ci.yml | 3 +--
test/test_workflow_local.sh | 2 +-
2 files changed, 2 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3040c3d..f0a8dce 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,10 +5,9 @@ before_script:
- conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV
- conda env create -f environment.yml
- conda activate mir_pipelines && echo $CONDA_DEFAULT_ENV
-
+ - cd test/
test:
script:
- - cd test
- bash test_workflow_local.sh
- bash test_dag.sh
- bash test_rule_graph.sh
diff --git a/test/test_workflow_local.sh b/test/test_workflow_local.sh
index f267712..7c234eb 100755
--- a/test/test_workflow_local.sh
+++ b/test/test_workflow_local.sh
@@ -24,7 +24,7 @@ snakemake \
--printshellcmds \
--snakefile="../snakemake/Snakefile" \
--use-singularity \
---singularity-args "--no-home --bind ${PWD},${PWD}/../images" \
+--singularity-args "--no-home --bind ${PWD},${PWD}/../../../projects,${PWD}/../images" \
--cores=4 \
--rerun-incomplete \
--configfile config.yaml \
--
GitLab