Merge branch 'SnakemakeReport' into 'dev'

Add Snakemake report

See merge request !64

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
 

install/environment.yml

 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
 

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 {})' \;

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 {})' \;