MTS-merino pipeline code review

.gitignore

@@ -1,3 +1,6 @@
+#Python compiled
+*.pyc
+
 # History files
 .Rhistory
 .Rapp.history
@@ -13,11 +16,12 @@
 
 # Output files from R CMD build
 /*.tar.gz
-
+.idea/
 # Output files from R CMD check
 /*.Rcheck/
 
 # RStudio files
+**.Rproj
 .Rproj.user/
 
 # produced vignettes
@@ -40,3 +44,32 @@ vignettes/*.pdf
 
 # pkgdown site
 docs/
+.idea/
+.ipynb_checkpoints/
+foo.json
+foo.sh
+enter_container.sh
+stack/enter_stack.sh
+stack/run*.sh
+extract-biomarkers/docker_run_*.sh
+
+# report files
+reports/rmarkdown/*.html
+screen_qc/rmarkdown/*.html
+landing_pages/rmarkdown/*.html
+node_modules
+__pycache__/
+
+# biomarker feature files
+biomarker_files/*.csv
+biomarker_data/*.csv
+
+#debug notebooks
+#*.ipynb
+
+#scratch folder
+scratch/
+wkdir/
+wkdir/*
+
+.DS_Store