################################################################################
##
## Copyright (c) 2007-2011 Illumina, Inc.
##
## This software is covered by the "Illumina Genome Analyzer Software
## License Agreement" and the "Illumina Source Code License Agreement",
## and certain third party copyright/licenses, and any user of this
## source file is bound by the terms therein (see accompanying files
## Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
## Illumina_Source_Code_License_Agreement.pdf and third party
## copyright/license notices).
##
## This file is part of the Consensus Assessment of Sequence And VAriation
## (CASAVA) software package.
##
## file FlowcellSummary.mk
##
## brief Produces whole-flowcell summary page.
##
## author Roman Petrovski
##
################################################################################

# make sure cat is used instead of copy for target file to get the default permission
# bits as opposite to inheriting the installation folder ones which are usually read-only
css/Reports.css: css/.sentinel
	$(CMDPREFIX) $(CAT) $(DATA_DIR)/Reports.css >$(SAFEPIPETARGET)

Flowcell_Summary_$(FLOWCELL).htm: Flowcell_$(SCORE_XML) Flowcell_$(RESCORE_XML) \
  $(foreach project, $(PROJECTS), $($(project)_SAMPLE_PAIR_XML_FILES)) config.xml \
  css/Reports.css \
  $(EXPT_DIR)/DemultiplexedBustardSummary.xml $(TEMP_DIR)/SampleSheet.xml
	$(CMDPREFIX) $(XSLTPROC) \
	--stringparam SAMPLE_SHEET_PATH_PARAM '$(CURDIR)/$(TEMP_DIR)/SampleSheet.xml' \
	--stringparam BUSTARD_SUMMARY_PATH_PARAM '$(EXPT_DIR)/DemultiplexedBustardSummary.xml' \
	--stringparam SCORE_XML_PARAM '$(CURDIR)/Flowcell_$(SCORE_XML)' \
	--stringparam RESCORE_XML_PARAM '$(CURDIR)/Flowcell_$(RESCORE_XML)' \
	--stringparam FLOWCELL_PARAM '$(FLOWCELL)' \
	$(DATA_DIR)/FlowcellSampleSummary.xsl config.xml > $(SAFEPIPETARGET)

.SECONDARY: $(TEMP_DIR)/SampleSheet.xml
$(TEMP_DIR)/SampleSheet.xml : SampleSheet.csv $(TEMP_DIR)/.sentinel
	$(CMDPREFIX) $(PRINT_SS_XML) --sample-sheet $< >$(SAFEPIPETARGET)

Flowcell_$(SCORE_XML): \
  $(foreach project, $(PROJECTS), $($(project)_SUMMARY_DIR)/$(SCORE_XML))
	$(CMDPREFIX) $(ECHO) '<?xml version="1.0"?><Stats/>' $(foreach part_summ, $^, \
		| $(XSLTPROC) --stringparam with $(part_summ) $(DATA_DIR)/MergeXmlDocuments.xsl -) \
	> $(SAFEPIPETARGET)

Flowcell_$(RESCORE_XML): \
  $(foreach project, $(PROJECTS), $($(project)_SUMMARY_DIR)/$(RESCORE_XML))
	$(CMDPREFIX) $(ECHO) '<?xml version="1.0"?><Stats/>' $(foreach part_summ, $^, \
		| $(XSLTPROC) --stringparam with $(part_summ) $(DATA_DIR)/MergeXmlDocuments.xsl -) \
	> $(SAFEPIPETARGET)