chipseq changes

example/dev/input/config.yaml

@@ -63,7 +63,6 @@ samples:
 
   # STRING. "ATACseq" or "ChIPseq". Only data type specific steps are executed. Currently, if set to ChIP-Seq, ATAC-seq specific steps like RSS adjustment are not executed.
   dataType: "ATACseq"
-  dataType: "ChIPseq"
 
 ###########################
 # SECTION additionalInput #

example/dev/input/samples.csv

-individual	sampleName	path_inputForward	path_inputReverse	Flowcell_ID	lane_ID	Technology	Library_ID	replicate_No
-"test1"	"test1_rep1"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep1_1.fastq.gz"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep1_2.fastq.gz"	"NA"	"NA"	"ILLUMINA"	"default"	"1"
-"test1"	"test1_rep2"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep2_1.fastq.gz"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep2_2.fastq.gz"	"NA"	"NA"	"ILLUMINA"	"default"	"1"
-"test2"	"test2_rep1"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test2_rep1_1.fastq.gz"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test2_rep1_2.fastq.gz"	"NA"	"NA"	"ILLUMINA"	"default"	"1"
+individual	sampleName	path_inputForward	path_inputReverse	Flowcell_ID	lane_ID	Technology	Library_ID	replicate_No control_sampleName
+"test1"	"test1_rep1"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep1_1.fastq.gz"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep1_2.fastq.gz"	"NA"	"NA"	"ILLUMINA"	"default"	"1"	"NA"
+"test1"	"test1_rep2"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep2_1.fastq.gz"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test1_rep2_2.fastq.gz"	"NA"	"NA"	"ILLUMINA"	"default"	"1"	"NA"
+"test2"	"test2_rep1"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test2_rep1_1.fastq.gz"	"/g/scb2/zaugg/carnold/Projects/AtacSeq/example/dev/input/data/test2_rep1_2.fastq.gz"	"NA"	"NA"	"ILLUMINA"	"default"	"1"	"NA"