# This makefile was automatically generated by CASAVA-1.8.2.
# Please do not edit.

# first target needs to be defined in the beginning. Ohterwise includes such as
# Log.mk cause unexpected behavior
firsttarget: all

BASECALLS_DIR:=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/Validation/100723_EAS346_0188_FC626BWAAXX/Data/Intensities/BaseCalls
INTENSITIES_DIR:=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/Validation/100723_EAS346_0188_FC626BWAAXX/Data/Intensities/BaseCalls/..
MAKEFILES_DIR:=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/makefiles

# Import the global configuration
include $(MAKEFILES_DIR)/Config.mk

include $(MAKEFILES_DIR)/Sentinel.mk

# Import the debug functionalities
include $(MAKEFILES_DIR)/Debug.mk

# Import the logging functionalities
include $(MAKEFILES_DIR)/Log.mk

# Setup:
BARCODE_CYCLES:=47 48 49 50 51 52 53 54
r1_CYCLES:=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
r1_DEMUX_CYCLES:=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
r1_ADAPTER:=''
r2_CYCLES:=56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101
r2_DEMUX_CYCLES:=47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
r2_ADAPTER:=''
ALL_ORIGINAL_CYCLES:=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101
INCLUDED_ORIGINAL_READS:=1 3
DEMUX_READS:=1 2
COMPRESSION:=gzip
FLOWCELL:=FC626BWAAXX
COMPRESSIONSUFFIX:=.gz
FILTER_PER_READ:=1
DEMUX_OPTIONS:= --filter-per-read --positions-format=.locs --fastq-cluster-count=4000000 --gz-level=1 --mismatches='0' --instrument-name='MONDAS33' --run-number='0188'

STATS_TO_SIGNAL_MEANS_OPTIONS:=

# Information extracted from SampleSheet.csv
include ./SampleSheet.mk
# this list gets populated by DemultiplexLaneRead.mk
ALL_DEMUX_SUMMARIES:=
post_run.done: l8.done l4.done DemultiplexedBustardSummary.xml DemultiplexedBustardConfig.xml Basecall_Stats_$(FLOWCELL)/Demultiplex_Stats.htm
	$(POST_RUN_COMMAND)

all: clean_intermediate.done
	@$(LOG_INFO)  $@ completed successfully.

r1_post_run.done: l8_r1.done l4_r1.done
	$(POST_RUN_COMMAND_R1)

r1: r1_post_run.done
	@$(LOG_INFO)  $@ completed successfully.

r2_post_run.done: l8_r2.done l4_r2.done
	$(POST_RUN_COMMAND_R2)

r2: r2_post_run.done
	@$(LOG_INFO)  $@ completed successfully.

# DEMULTIPLEXING:

TILES_FILTER := 

l8_TILES:=0005 0015
lane:=8
include $(MAKEFILES_DIR)/DemultiplexLane.mk

l4_TILES:=0005 0015
lane:=4
include $(MAKEFILES_DIR)/DemultiplexLane.mk


include $(MAKEFILES_DIR)/DemultiplexFlowCell.mk

.PHONY: self_test
self_test: DemultiplexedBustardConfig.xml
	@$(LOG_INFO) $@ completed successfully.;