digraph workflow {
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			rects="812,313.5,922,332.5",
			width=1.5278];
	}
	subgraph cluster_outputs {
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			lp="997,17.5",
			lwidth=1.28,
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			fillcolor="#94DDF4",
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			label=vcf,
			pos="1081,45",
			rects="1065,35.5,1097,54.5",
			width=0.44444];
		gathered_directory	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 951.5 35.5 951.5 54.5 1060.5 54.5 1060.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1006 42.5 0 93 18 -gathered_directory ",
			fillcolor="#94DDF4",
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			pos="1006,45",
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			width=1.5139];
		cpg_bigwig	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1189.5 35.5 1189.5 54.5 1260.5 54.5 1260.5 35.5 ",
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		cram	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1101.5 35.5 1101.5 54.5 1142.5 54.5 1142.5 35.5 ",
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		cpgs	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1146.5 35.5 1146.5 54.5 1185.5 54.5 1185.5 35.5 ",
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			rects="1146.5,35.5,1185.5,54.5",
			width=0.54167];
	}
	bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 683.5 260.5 683.5 279.5 926.5 279.5 926.5 260.5 ",
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		pos="805,270",
		rects="683.5,260.5,926.5,279.5",
		width=3.375];
	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 960.72 313.55 949.01 310.51 935.45 307.28 923 305 893.07 299.52 883.26 308.3 855 297 848.81 294.53 848.75 291.38 \
843 288 839.99 286.23 836.76 284.52 833.5 282.91 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 864.5 290.6 0 19 3 -bam ",
		label=bam,
		lp="864.5,292.5",
		pos="e,825.93,279.36 960.72,313.55 949.01,310.51 935.45,307.28 923,305 893.07,299.52 883.26,308.3 855,297 848.81,294.53 848.75,291.38 \
843,288 839.99,286.23 836.76,284.52 833.5,282.91"];
	bisulfite_qc	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 946.5 125.5 946.5 144.5 1047.5 144.5 1047.5 125.5 ",
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		label="Bisulfite QC tools",
		pos="997,135",
		rects="946.5,125.5,1047.5,144.5",
		width=1.4028];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 64.53 313.5 71.33 303.78 81 287.12 81 271 81 271 81 271 81 179 81 135.91 736.23 134.95 938.35 135.68 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 938.25 138.13 945.26 135.7 938.27 133.23 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 109.5 223.1 0 57 12 -QCannotation ",
		label=QCannotation,
		lp="109.5,225",
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	bam_to_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1114 170.5 1114 189.5 1254 189.5 1254 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1184 177.5 0 124 22 -BAM to CRAM conversion ",
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		label="BAM to CRAM conversion",
		pos="1184,180",
		rects="1114,170.5,1254,189.5",
		width=1.9444];
	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 7 1197.88 313.67 1197.6 299.25 1196.71 268.67 1194 243 1192.36 227.47 1189.42 209.91 1187.16 197.45 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1189.62 197.3 1185.93 190.87 1184.8 198.2 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1214 245.6 0 40 9 -reference ",
		label=reference,
		lp="1214,247.5",
		pos="e,1185.7,189.38 1197.9,313.67 1197.6,299.25 1196.7,268.67 1194,243 1192.4,227.47 1189.4,209.91 1187.2,197.45"];
	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 1173.16 313.62 1122.13 296.32 1009.71 257.82 1003 252 974.92 227.66 984.16 178.26 991.54 152.48 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 993.85 153.29 993.56 145.88 989.17 151.85 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1010 223.1 0 40 9 -reference ",
		label=reference,
		lp="1010,225",
		pos="e,994.01,144.43 1173.2,313.62 1122.1,296.32 1009.7,257.82 1003,252 974.92,227.66 984.16,178.26 991.54,152.48"];
	pileup	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1026.5 170.5 1026.5 189.5 1109.5 189.5 1109.5 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1068 177.5 0 67 14 -Biscuit pileup ",
		height=0.27778,
		label="Biscuit pileup",
		pos="1068,180",
		rects="1026.5,170.5,1109.5,189.5",
		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 10 1191 313.54 1180.96 300.95 1162.63 276.16 1153 252 1146.81 236.45 1156.44 228.08 1146 215 1137.84 204.77 1125.98 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1114.92 190.22 1107.5 189.99 1113.16 194.79 ",
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		label=reference,
		lp="1173,247.5",
		pos="e,1106.1,189.45 1191,313.54 1181,300.95 1162.6,276.16 1153,252 1146.8,236.45 1156.4,228.08 1146,215 1137.8,204.77 1126,197.55 1114,\
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	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 1177.01 313.52 1167.93 310.25 1157.1 306.85 1147 305 1103.9 297.11 991.28 311.7 950 297 943.72 294.76 944.18 290.51 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 920.05 279.3 912.66 279.88 918.8 284.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 983 290.6 0 66 15 -reference_index ",
		label=reference_index,
		lp="983,292.5",
		pos="e,911.2,279.5 1177,313.52 1167.9,310.25 1157.1,306.85 1147,305 1103.9,297.11 991.28,311.7 950,297 943.72,294.76 944.18,290.51 938,\
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	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1091 125.5 1091 144.5 1473 144.5 1473 125.5 ",
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		label="convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script",
		pos="1282,135",
		rects="1091,125.5,1473,144.5",
		width=5.3056];
	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 1222.18 313.55 1239.94 305.62 1261 291.83 1261 271 1261 271 1261 271 1261 179 1261 168.95 1265.69 158.8 1270.64 \
150.88 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1272.35 152.72 1274.27 145.56 1268.3 149.96 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1281 223.1 0 40 9 -reference ",
		label=reference,
		lp="1281,225",
		pos="e,1275.1,144.31 1222.2,313.55 1239.9,305.62 1261,291.83 1261,271 1261,271 1261,271 1261,179 1261,168.95 1265.7,158.8 1270.6,150.88"];
	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 1083.71 313.54 1075.35 310.27 1065.36 306.86 1056 305 1018.26 297.48 919.22 310.01 883 297 876.73 294.75 877.01 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 856.63 279.59 849.21 279.85 855.17 284.27 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 912 290.6 0 58 13 -read_group_id ",
		label=read_group_id,
		lp="912,292.5",
		pos="e,847.77,279.4 1083.7,313.54 1075.4,310.27 1065.4,306.86 1056,305 1018.3,297.48 919.22,310.01 883,297 876.73,294.75 877.01,290.89 \
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	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 313.27 313.57 347.43 305.55 401.5 293.85 449 288 523.65 278.8 607.68 274.51 675.34 272.53 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 675.07 274.99 682 272.35 674.93 270.09 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 492 290.6 0 86 19 -adapter_min_overlap ",
		label=adapter_min_overlap,
		lp="492,292.5",
		pos="e,683.51,272.3 313.27,313.57 347.43,305.55 401.5,293.85 449,288 523.65,278.8 607.68,274.51 675.34,272.53"];
	trimming_adapter_trim_end -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 472 313.54 498.47 305.6 540.11 294.08 577 288 608.68 282.78 643.11 279.16 675.38 276.66 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 675.23 279.12 682.03 276.15 674.86 274.24 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 613 290.6 0 72 16 -adapter_trim_end ",
		label=adapter_trim_end,
		lp="613,292.5",
		pos="e,683.54,276.04 472,313.54 498.47,305.6 540.11,294.08 577,288 608.68,282.78 643.11,279.16 675.38,276.66"];
	assay_non_cpg_sites -> vcf2bed	[_draw_="c 7 -#000000 B 10 1309 313.7 1309 303.6 1309 286.05 1309 271 1309 271 1309 271 1309 179 1309 168.26 1302.88 158 1296.47 150.2 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1298.65 148.96 1292.15 145.39 1295.01 152.23 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1352 223.1 0 86 19 -assay_non_cpg_sites ",
		label=assay_non_cpg_sites,
		lp="1352,225",
		pos="e,1291.1,144.26 1309,313.7 1309,303.6 1309,286.05 1309,271 1309,271 1309,271 1309,179 1309,168.26 1302.9,158 1296.5,150.2"];
	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 610.26 313.51 626.94 305.67 653.12 294.31 677 288 687.64 285.19 698.9 282.83 710.16 280.86 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 710.36 283.31 716.86 279.73 709.55 278.47 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 705.5 290.6 0 57 12 -max_uncalled ",
		label=max_uncalled,
		lp="705.5,292.5",
		pos="e,718.35,279.48 610.26,313.51 626.94,305.67 653.12,294.31 677,288 687.64,285.19 698.9,282.83 710.16,280.86"];
	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1198 80.5 1198 99.5 1366 99.5 1366 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1282 87.5 0 152 29 -bedGraph to bigwig conversion ",
		height=0.27778,
		label="bedGraph to bigwig conversion",
		pos="1282,90",
		rects="1198,80.5,1366,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 10 1441.71 313.66 1459.06 305.66 1480 291.71 1480 271 1480 271 1480 271 1480 134 1480 110.46 1425.88 99.78 1374.23 \
94.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1374.67 92.53 1367.48 94.36 1374.24 97.41 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1512.5 200.6 0 65 15 -reference_sizes ",
		label=reference_sizes,
		lp="1512.5,202.5",
		pos="e,1366,94.223 1441.7,313.66 1459.1,305.66 1480,291.71 1480,271 1480,271 1480,271 1480,134 1480,110.46 1425.9,99.781 1374.2,94.949"];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 734.57 313.69 733.76 306.09 733.91 294.99 740 288 741.24 286.57 742.59 285.25 744.03 284.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 745.19 286.22 749.56 280.23 742.41 282.18 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 772 290.6 0 64 14 -min_readlength ",
		label=min_readlength,
		lp="772,292.5",
		pos="e,750.81,279.37 734.57,313.69 733.76,306.09 733.91,294.99 740,288 741.24,286.57 742.59,285.25 744.03,284.04"];
	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 832.17 313.57 823.4 309.85 814.84 304.55 809 297 806.86 294.23 805.64 290.8 804.99 287.34 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 807.45 287.35 804.43 280.57 802.56 287.75 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 827.5 290.6 0 37 8 -adapters ",
		label=adapters,
		lp="827.5,292.5",
		pos="e,804.31,279.06 832.17,313.57 823.4,309.85 814.84,304.55 809,297 806.86,294.23 805.64,290.8 804.99,287.34"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1062.5 80.5 1062.5 99.5 1181.5 99.5 1181.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1122 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="1122,90",
		rects="1062.5,80.5,1181.5,99.5",
		width=1.6528];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 7 1134.25 170.53 1106.65 164.71 1076.27 156.04 1068 145 1056.21 129.26 1076.21 113.63 1095.12 103.27 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1096.08 105.53 1101.17 100.13 1093.83 101.18 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1078.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="1078.5,135",
		pos="e,1102.5,99.436 1134.2,170.53 1106.7,164.71 1076.3,156.04 1068,145 1056.2,129.26 1076.2,113.63 1095.1,103.27"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 4 997.86 125.56 999.34 111.14 1002.37 81.48 1004.29 62.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1006.72 63 1005 55.79 1001.85 62.5 ",
		pos="e,1005.2,54.284 997.86,125.56 999.34,111.14 1002.4,81.476 1004.3,62.727"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 7 1065.76 170.62 1061.53 153.34 1053.49 112.66 1062 80 1063.69 73.52 1066.91 66.97 1070.23 61.37 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1072.15 62.91 1073.87 55.69 1068.03 60.27 ",
		pos="e,1074.7,54.418 1065.8,170.62 1061.5,153.34 1053.5,112.66 1062,80 1063.7,73.522 1066.9,66.969 1070.2,61.369"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 1052.96 170.67 1048.15 167.96 1042.83 164.89 1038 162 1030.99 157.8 1023.41 153.05 1016.7 148.77 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1018.31 146.89 1011.1 145.18 1015.67 151.02 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1044.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="1044.5,157.5",
		pos="e,1009.8,144.36 1053,170.67 1048.2,167.96 1042.8,164.89 1038,162 1031,157.8 1023.4,153.05 1016.7,148.77"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 4 1109.26 170.71 1144.15 163.7 1194.27 153.63 1231.54 146.14 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1231.9 148.57 1238.28 144.78 1230.94 143.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1200.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="1200.5,157.5",
		pos="e,1239.8,144.49 1109.3,170.71 1144.2,163.7 1194.3,153.63 1231.5,146.14"];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 1122 80.71 1122 75.59 1122 68.85 1122 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1124.45 62.78 1122 55.78 1119.55 62.78 ",
		pos="e,1122,54.265 1122,80.709 1122,75.593 1122,68.848 1122,62.666"];
	bedgraph_to_bigwig -> cpg_bigwig	[_draw_="c 7 -#000000 B 4 1270.74 80.5 1262.78 74.5 1251.94 66.32 1242.81 59.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1244.51 57.65 1237.45 55.39 1241.56 61.56 ",
		pos="e,1236.2,54.478 1270.7,80.505 1262.8,74.497 1251.9,66.32 1242.8,59.435"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1036 215.5 1036 234.5 1146 234.5 1146 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1091 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="1091,225",
		rects="1036,215.5,1146,234.5",
		width=1.5278];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 861.91 260.52 905.77 253.97 968.17 244.64 1027.67 235.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1027.99 238.08 1034.54 234.61 1027.26 233.24 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 986.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="986.5,247.5",
		pos="e,1036,234.39 861.91,260.52 905.77,253.97 968.17,244.64 1027.7,235.65"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 1109.37 215.5 1123.26 209.09 1142.5 200.19 1157.97 193.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1158.97 195.27 1164.29 190.11 1156.91 190.83 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1154.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="1154.5,202.5",
		pos="e,1165.7,189.48 1109.4,215.5 1123.3,209.09 1142.5,200.19 1158,193.04"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 1046.76 215.6 1031.72 210.59 1016.16 202.63 1006 190 1001.45 184.35 999.13 166.25 997.99 152.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1000.46 152.68 997.52 145.87 995.57 153.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1015.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="1015.5,180",
		pos="e,997.41,144.36 1046.8,215.6 1031.7,210.59 1016.2,202.63 1006,190 1001.5,184.35 999.13,166.25 997.99,152.55"];
	merge -> pileup	[_draw_="c 7 -#000000 B 4 1086.57 215.71 1083.64 210.24 1079.71 202.9 1076.23 196.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1078.6 195.62 1073.13 190.6 1074.28 197.93 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1090.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="1090.5,202.5",
		pos="e,1072.4,189.27 1086.6,215.71 1083.6,210.24 1079.7,202.9 1076.2,196.38"];
	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 7 1246.45 125.6 1230 120.34 1211.04 112.19 1197 100 1190.65 94.49 1180.58 75.75 1173.65 61.89 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1175.94 60.99 1170.65 55.78 1171.54 63.15 ",
		pos="e,1170,54.426 1246.5,125.6 1230,120.34 1211,112.19 1197,100 1190.7,94.49 1180.6,75.753 1173.6,61.889"];
	vcf2bed -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 4 1282 125.71 1282 120.59 1282 113.85 1282 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1284.45 107.78 1282 100.78 1279.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1328.5 110.6 0 93 20 -methylation_bedgraph ",
		label=methylation_bedgraph,
		lp="1328.5,112.5",
		pos="e,1282,99.265 1282,125.71 1282,120.59 1282,113.85 1282,107.67"];
}