From f7cda54618ed6119cd8d185d47f60be643a6abbc Mon Sep 17 00:00:00 2001
From: BIOPZ-Bak Maciej <maciej.bak@unibas.ch>
Date: Fri, 12 Jun 2020 18:36:14 +0200
Subject: [PATCH] Add Snakemake report
---
install/environment.root.yml | 6 +++++-
install/environment.yml | 7 ++++++-
tests/test_integration_workflow/test.local.sh | 9 +++++++++
tests/test_integration_workflow/test.slurm.sh | 9 +++++++++
4 files changed, 29 insertions(+), 2 deletions(-)
diff --git a/install/environment.root.yml b/install/environment.root.yml
index 20075ba..acfbe7e 100644
--- a/install/environment.root.yml
+++ b/install/environment.root.yml
@@ -4,10 +4,14 @@ channels:
- defaults
dependencies:
- graphviz=2.40.1
+ - jinja2=2.11.2
+ - networkx=2.4
- pip=20.0.2
+ - pygments=2.6.1
+ - pygraphviz=1.3
- python=3.7.4
- singularity=3.5.2
- pip:
- pandas==1.0.1
- - snakemake==5.10.0
+ - snakemake==5.19.2
diff --git a/install/environment.yml b/install/environment.yml
index 1f69c61..8fcba7a 100644
--- a/install/environment.yml
+++ b/install/environment.yml
@@ -1,11 +1,16 @@
name: zarp
channels:
+ - conda-forge
- defaults
dependencies:
- graphviz=2.40.1
+ - jinja2=2.11.2
+ - networkx=2.4
- pip=20.0.2
+ - pygments=2.6.1
+ - pygraphviz=1.3
- python=3.7.4
- pip:
- pandas==1.0.1
- - snakemake==5.10.0
+ - snakemake==5.19.2
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 16d7157..883424d 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -3,11 +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
cd $user_dir
echo "Exit status: $rc"
}
@@ -32,6 +35,12 @@ snakemake \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose
+# Create a Snakemake report after the workflow execution
+snakemake \
+ --snakefile="../../Snakefile" \
+ --configfile="../input_files/config.yaml" \
+ --report="snakemake_report.html"
+
# Check md5 sum of some output files
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index fef99cc..0145ae7 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -3,11 +3,14 @@
# Tear down test environment
cleanup () {
rc=$?
+ 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
cd $user_dir
echo "Exit status: $rc"
}
@@ -34,6 +37,12 @@ snakemake \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose
+# Create a Snakemake report after the workflow execution
+snakemake \
+ --snakefile="../../Snakefile" \
+ --configfile="../input_files/config.yaml" \
+ --report="snakemake_report.html"
+
# Check md5 sum of some output files
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
--
GitLab