chore: update .gitignore from template

.gitignore

@@ -1 +1,55 @@
 docs/user-guide/site/
+
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+replay_pid*
+
+# nextflow
+.nextflow*
+/work*/
+/data/
+/results/
+/output/
+/params.yaml
+
+# python packaging
+*.pyc
+*.egg-info
+/build
+
+# macOS
+.DS_Store
+
+# code editors
+.vscode/
+*.code-workspace
+
+# user-specific dev files
+*KLS*
+*.Rproj
+.Rproj.user
+.Rhistory
+
+/submit_slurm.sh
+/tmp/