Updated read counts to give information about aligment percent, and adapter percent.

[htsworkflow.git] / htswanalysis / scripts / Flowcell_QC_Makefile

diff --git a/htswanalysis/scripts/Flowcell_QC_Makefile b/htswanalysis/scripts/Flowcell_QC_Makefile
index f57061ddeb0d322989e34007365d8c7f4636b38f..4216db16b5583fbd74b99305c8eaf1de2af51d5c 100644 (file)
--- a/htswanalysis/scripts/Flowcell_QC_Makefile
+++ b/htswanalysis/scripts/Flowcell_QC_Makefile
@@ -16,10 +16,9 @@ all: $(QPCR_FILES) $(PROFILE_FILES) $(CMPLX_FILES) $(PROFILE_IMAGES) $(PERCENT_B
        $(EXPTRACK_DIR)/bin/complexity_count `basename $<` $< > $@
 
 %.txt.count: %.txt
-       grep -v contam $< | awk '{if(NF > 3) {print $$1} }' | wc -l > $@;
+       $(EXPTRACK_DIR)/scripts/count_reads.pm $< $(shell echo $< | awk -F\. '{ print $$1".all.txt.gz"; }') > $@
 
 %.txt.qPCR: %.txt
-       echo $(EXPTRACK_DIR)/bin/qPCR $< $(EXPTRACK_DIR)/reference_data/GenericBackground $(EXPTRACK_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r | awk -F\/ '{print $$NF}'
        $(EXPTRACK_DIR)/bin/qPCR $< $(EXPTRACK_DIR)/reference_data/GenericBackground $(EXPTRACK_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r | awk -F\/ '{print $$NF}' > $@
 
 %.txt.profile: %.txt