From 918714cddd66f0e4b8aae950bd8fb186e6209644 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Tue, 13 Jul 2021 13:07:20 +0200
Subject: [PATCH] Fix paths to Snakefile for slurm test scripst
---
tests/test_integration_workflow/test.slurm.sh | 4 ++--
.../test.slurm.sh | 4 ++--
.../test.slurm.sh | 20 +++++++++----------
3 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index c6c8410..6c40abb 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -26,7 +26,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--cluster-config="../input_files/cluster.json" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -41,7 +41,7 @@ snakemake \
# Create a Snakemake report after the workflow execution
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--report="snakemake_report.html"
diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
index 74ba028..10a2752 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
@@ -26,7 +26,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.mutliple_lanes.yml" \
--cluster-config="../input_files/cluster.json" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -41,7 +41,7 @@ snakemake \
# Create a Snakemake report after the workflow execution
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.mutliple_lanes.yml" \
--report="snakemake_report.html"
diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
index e4a7009..873f17b 100755
--- a/tests/test_integration_workflow_with_conda/test.slurm.sh
+++ b/tests/test_integration_workflow_with_conda/test.slurm.sh
@@ -3,14 +3,14 @@
# Tear down test environment
cleanup () {
rc=$?
- # rm -rf .cache/
- # rm -rf .config/
- # rm -rf .fontconfig/
- # rm -rf .java/
- # rm -rf .snakemake/
- # rm -rf logs/
- # rm -rf results/
- # rm -rf snakemake_report.html
+ rm -rf .cache/
+ rm -rf .config/
+ rm -rf .fontconfig/
+ rm -rf .java/
+ rm -rf .snakemake/
+ rm -rf logs/
+ rm -rf results/
+ rm -rf snakemake_report.html
cd $user_dir
echo "Exit status: $rc"
}
@@ -26,7 +26,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--cluster-config="../input_files/cluster.json" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -40,7 +40,7 @@ snakemake \
# Create a Snakemake report after the workflow execution
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--report="snakemake_report.html"
--
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