Resolve "Update deeptools"

Closes #6 (closed)

Adds back Deeptools for QC steps

test_data/design_ENCSR238SGC_SE.txt

 sample_id	experiment_id	biosample	factor	treatment	replicate	control_id	fastq_read1
-ENCBS844FSC	ENCSR238SGC	limb	H3K4me1	None	1	ENCBS844FSC	ENCFF833BLU.fastq.gz
-ENCBS892NXC	ENCSR238SGC	limb	H3K4me1	None	2	ENCBS892NXC	ENCFF646LXU.fastq.gz
-ENCBS844FSC	ENCSR687ALB	limb	Control	None	1	ENCBS844FSC	ENCFF524CAC.fastq.gz
-ENCBS892NXC	ENCSR687ALB	limb	Control	None	2	ENCBS892NXC	ENCFF163AJI.fastq.gz
+ENCLB144FDT	ENCSR238SGC	limb	H3K4me1	None	1	ENCLB304SBJ	ENCFF833BLU.fastq.gz
+ENCLB831RUI	ENCSR238SGC	limb	H3K4me1	None	2	ENCLB410VVO	ENCFF646LXU.fastq.gz
+ENCLB304SBJ	ENCSR687ALB	limb	Control	None	1	ENCLB304SBJ	ENCFF524CAC.fastq.gz
+ENCLB410VVO	ENCSR687ALB	limb	Control	None	2	ENCLB410VVO	ENCFF163AJI.fastq.gz