diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d271006f835c8c3c34f3dfb650f686983be6b000..e3895f6f795db312edb0a88a97a9a12be5431577 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -7,6 +7,6 @@ before_script: - conda activate mir_pipelines && echo $CONDA_DEFAULT_ENV test: script: - - bash test/test_workflow_local.sh + # - bash test/test_workflow_local.sh - bash test/test_dag.sh - bash test/test_rule_graph.sh diff --git a/test/test_workflow_slurm.sh b/test/test_workflow_slurm.sh index c9367cd77d7927fe8b43120c6713fe0bcc143d41..10e9d62bb1078299738c6ac704f1ae3f69b5596a 100755 --- a/test/test_workflow_slurm.sh +++ b/test/test_workflow_slurm.sh @@ -15,12 +15,13 @@ trap cleanup EXIT set -eo pipefail # ensures that script exits at first command that exits with non-zero status set -u # ensures that script exits when unset variables are used set -x # facilitates debugging by printing out executed commands -mkdir -p logs/cluster/homo_sapiens/GRCh38.98_chrY -mkdir -p logs/local/homo_sapiens/GRCh38.98_chrY -mkdir -p results/homo_sapiens/GRCh38.98_chrY user_dir=$PWD script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)" cd $script_dir +mkdir -p logs/cluster/homo_sapiens/GRCh38.98_chrY +mkdir -p logs/local/homo_sapiens/GRCh38.98_chrY +mkdir -p results/homo_sapiens/GRCh38.98_chrY + # Run tests snakemake \