# 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/110120_P20_0993_A805CKABXX/Data/Intensities/BaseCalls
INTENSITIES_DIR:=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/Validation/110120_P20_0993_A805CKABXX/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:=102 103 104 105 106 107
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 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
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 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
r1_ADAPTER:=''
r2_CYCLES:=109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184
r2_DEMUX_CYCLES:=77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152
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 76 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184
INCLUDED_ORIGINAL_READS:=1 3
DEMUX_READS:=1 2
COMPRESSION:=gzip
FLOWCELL:=A805CKABXX
COMPRESSIONSUFFIX:=.gz
DEMUX_OPTIONS:= --need-separate-controls --fastq-cluster-count=4000000 --gz-level=1 --mismatches='0' --instrument-name='HWI-BRUNOP20X' --run-number='0993'

STATS_TO_SIGNAL_MEANS_OPTIONS:= --need-separate-controls

# Information extracted from SampleSheet.csv
include ./SampleSheet.mk
# this list gets populated by DemultiplexLaneRead.mk
ALL_DEMUX_SUMMARIES:=
post_run.done: l1.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: l1_r1.done
	$(POST_RUN_COMMAND_R1)

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

r2_post_run.done: l1_r2.done
	$(POST_RUN_COMMAND_R2)

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

# DEMULTIPLEXING:

TILES_FILTER := 

l1_TILES:=1204
lane:=1
include $(MAKEFILES_DIR)/DemultiplexLane.mk


include $(MAKEFILES_DIR)/DemultiplexFlowCell.mk

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