From 5aa652231e6f796528890842116414b0eaf06596 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Mon, 19 Oct 2020 10:52:17 +0200
Subject: [PATCH] use --notemp for CI tests
---
tests/test_alfa/test.sh | 1 +
tests/test_create_dag_image/test.sh | 1 +
tests/test_create_rule_graph/test.sh | 1 +
tests/test_integration_workflow/test.local.sh | 1 +
tests/test_integration_workflow/test.slurm.sh | 1 +
tests/test_integration_workflow_multiple_lanes/test.local.sh | 1 +
tests/test_integration_workflow_multiple_lanes/test.slurm.sh | 1 +
7 files changed, 7 insertions(+)
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 1472685..5e417f4 100755
--- a/tests/test_alfa/test.sh
+++ b/tests/test_alfa/test.sh
@@ -33,6 +33,7 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose \
+ --notemp \
results/ALFA/ALFA_plots_mqc.png
# Check md5 sum of some output files
diff --git a/tests/test_create_dag_image/test.sh b/tests/test_create_dag_image/test.sh
index afd8de4..c5fc8dd 100755
--- a/tests/test_create_dag_image/test.sh
+++ b/tests/test_create_dag_image/test.sh
@@ -26,5 +26,6 @@ snakemake \
--printshellcmds \
--dryrun \
--verbose \
+ --notemp \
| dot -Tsvg > "../../images/dag_test_workflow.svg"
diff --git a/tests/test_create_rule_graph/test.sh b/tests/test_create_rule_graph/test.sh
index 51e5383..2fa3db7 100755
--- a/tests/test_create_rule_graph/test.sh
+++ b/tests/test_create_rule_graph/test.sh
@@ -26,5 +26,6 @@ snakemake \
--printshellcmds \
--dryrun \
--verbose \
+ --notemp \
| dot -Tsvg > "../../images/rule_graph.svg"
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 883424d..00f6d96 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -33,6 +33,7 @@ snakemake \
--rerun-incomplete \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
+ --notemp \
--verbose
# Create a Snakemake report after the workflow execution
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 0145ae7..02aaf72 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -35,6 +35,7 @@ snakemake \
--rerun-incomplete \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
+ --notemp \
--verbose
# Create a Snakemake report after the workflow execution
diff --git a/tests/test_integration_workflow_multiple_lanes/test.local.sh b/tests/test_integration_workflow_multiple_lanes/test.local.sh
index 018b47d..9804f33 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.local.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.local.sh
@@ -33,6 +33,7 @@ snakemake \
--rerun-incomplete \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
+ --notemp \
--verbose
# Create a Snakemake report after the workflow execution
diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
index f2dd459..a0517fd 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
@@ -35,6 +35,7 @@ snakemake \
--rerun-incomplete \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
+ --notemp \
--verbose
# Create a Snakemake report after the workflow execution
--
GitLab