better test script structure

.github/workflows/run-snakemake.yml

@@ -41,7 +41,7 @@ jobs:
         shell: bash -el {0}
         run: |
           pushd tests
-          bash -el test.sh
+          bash -el test.sh --quick
           popd
 
       - name: cat all log files on failure

acanthophis/template/config.yml

@@ -114,8 +114,8 @@ samplesets:
       callers:
         - mpileup
         - freebayes
-        # Deepvariant is disabled for Github actions tests, as it requires too much disk space
-        #- deepvariant
+        - deepvariant
+
       # Which short read aligners to use for variant calling? (can be
       # more/less/different to the align section above)
       aligners:

tests/setup.sh

@@ -1,11 +1,9 @@
 #!/bin/bash
 mamba env update -f environment-setup.yml
 conda activate acanthophis-tests
+set -xeuo pipefail
 rm -rf output/ tmp/
 mkdir -p output/ tmp/ rawdata/
 touch output/nobackup tmp/nobackup rawdata/nobackup
-python3 -m pip install -e ../
-set -xeuo pipefail
-snakemake --version
-snakemake --snakefile Snakefile.generate-rawdata -j 4 --software-deployment-method conda
+snakemake --snakefile Snakefile.generate-rawdata -j $(nproc 2>/dev/null || echo 2) --software-deployment-method conda
 tree rawdata

tests/test.sh

@@ -1,11 +1,28 @@
 #!/bin/bash
 set -euo pipefail
+
+# Reinstall acanthophis from git
 conda activate acanthophis-tests
 python3 -m pip uninstall --yes acanthophis
 python3 -m pip install -e ..
+
+# re-init after reinstall
 acanthophis-init --yes
+
+# recreate the conda env
 mamba env update -f environment.yml
 conda activate acanthophis
+
+# Clear outputs
 rm -fr output tmp
-set -x
+touch output/nobackup tmp/nobackup
+
+# If quick, overwrite config with cut-back version
+if [[ "$1" == "--quick" ]]
+then
+    cp .config_quick.yml config.yml
+    shift
+fi
+
+# Run pipeline
 snakemake -j $(nproc 2>/dev/null || echo 2)  --software-deployment-method conda --ri "${@}"