# This makefile was automatically generated by bcl2fastq-1.8.4.
# Please do not edit.

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

BASECALLS_DIR:=/ngs-seqdata/HiSeq/151218_SN1123_0456_AHFYH7BCXX/Data/Intensities/BaseCalls
INTENSITIES_DIR:=/ngs-seqdata/HiSeq/151218_SN1123_0456_AHFYH7BCXX/Data/Intensities/BaseCalls/..
MAKEFILES_DIR:=/usr/local/share/bcl2fastq-1.8.4/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:=52 53 54 55 56 57 60 61 62 63 64
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
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
r1_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
INCLUDED_ORIGINAL_READS:=1
DEMUX_READS:=1
COMPRESSION:=gzip
FLOWCELL:=HFYH7BCXX
COMPRESSIONSUFFIX:=.gz
DEMUX_OPTIONS:= --no-eamss  --need-separate-controls --positions-format=.clocs --fastq-cluster-count=0 --gz-level=1 --mismatches='1' --instrument-name='GWZHISEQ01' --run-number='0456'

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.

# DEMULTIPLEXING:

TILES_FILTER := 

l1_TILES:=1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216
lane:=1
include $(MAKEFILES_DIR)/DemultiplexLane.mk


include $(MAKEFILES_DIR)/DemultiplexFlowCell.mk

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