BUG: Fix batch mode with CellProfiler "Group"

- Set group to Well + Plate.
- Cleaned up pipeline.

Makefile

@@ -8,7 +8,7 @@
 
 # Overwritable paths to executables
 CELLPROFILER := cellprofiler
-PARALLEL := parallel
+PARALLEL := parallel --eta
 PYTHON := python
 RSCRIPT := Rscript
 
@@ -31,14 +31,27 @@ TARGETS_cellprofiler_batch := results/cellprofiler/Batch_data.h5
 SOURCES_cellprofiler_commands := $(TARGETS_cellprofiler_batch)
 TARGETS_cellprofiler_commands := results/cellprofiler/batch_commands.sh
 SOURCES_cellprofiler_headless := $(TARGETS_cellprofiler_commands)
-TARGETS_cellprofiler_db := results/cellprofiler/all-plates.db
-TARGETS_cellprofiler_prop := results/cellprofiler/all-plates.properties
+TARGETS_cellprofiler_db := results/cellprofiler/rnai-screen-tf.db
+TARGETS_cellprofiler_prop := results/cellprofiler/rna-screen-tf.properties
 TARGETS_cellprofiler := $(TARGETS_cellprofiler_db) $(TARGETS_cellprofiler_prop)
-define CELLPROFILER_OPTS
---pipeline=$(SOURCES_cellprofiler_pipe) \
+define CELLPROFILER_OPTS_COMMON
 --file-list=$(SOURCES_cellprofiler_filelist) \
 --output-directory=$(dir $(TARGETS_cellprofiler_db))
 endef
+define CELLPROFILER_OPTS_GUI
+$(CELLPROFILER_OPTS_COMMON) \
+--pipeline=$(SOURCES_cellprofiler_pipe)
+endef
+define CELLPROFILER_OPTS_BATCH
+$(CELLPROFILER_OPTS_COMMON) \
+--pipeline=$(SOURCES_cellprofiler_pipe) \
+--run-headless
+endef
+define CELLPROFILER_OPTS_HEADLESS
+$(CELLPROFILER_OPTS_COMMON) \
+--pipeline=$(SOURCES_cellprofiler_commands) \
+--run-headless
+endef
 SOURCES_signif_wells := $(TARGETS_cellprofiler_db)
 TARGETS_signif_wells := results/tables/rnai-p_values.csv
 SOURCES_plot_overlap := $(TARGETS_signif_wells)
@@ -82,14 +95,14 @@ $(call singleton,$(TARGETS_cellprofiler)) : $(SOURCES_cellprofiler_headless)
 	$(PARALLEL) :::: $<
 
 $(TARGETS_cellprofiler_commands) : $(SOURCES_cellprofiler_commands)
-	$(CELLPROFILER) --get-batch-commands=$< | sed 's#^CellProfiler#$(CELLPROFILER)#' | sort -nk 8.14 > $@
+	$(CELLPROFILER) $(CELLPROFILER_OPTS_HEADLESS) --get-batch-commands=$< | sed 's#^CellProfiler#$(CELLPROFILER)#' | sort -nk 8 > $@
 
 $(TARGETS_cellprofiler_batch) : $(SOURCES_cellprofiler)
-	$(CELLPROFILER) $(CELLPROFILER_OPTS) --run-headless
+	$(CELLPROFILER) $(CELLPROFILER_OPTS_BATCH)
 
 .PHONY : gui-cellprofiler
 gui-cellprofiler : $(SOURCES_cellprofiler) ## Interactively run CellProfiler.
-	$(CELLPROFILER) $(CELLPROFILER_OPTS)
+	$(CELLPROFILER) $(CELLPROFILER_OPTS_GUI)
 
 $(TARGETS_img_filelist) : $(abspath $(SOURCES_img_filelist))
 	find $< -type f | sort > $@