digraph workflow {
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		trimming_min_readlength	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 103.5 313.5 103.5 332.5 246.5 332.5 246.5 313.5 ",
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	subgraph cluster_outputs {
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			width=0.56944];
		gathered_directory	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 897.5 35.5 897.5 54.5 1006.5 54.5 1006.5 35.5 ",
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		cpgs	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1092.5 35.5 1092.5 54.5 1131.5 54.5 1131.5 35.5 ",
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			width=0.54167];
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		cpg_bigwig	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1135.5 35.5 1135.5 54.5 1206.5 54.5 1206.5 35.5 ",
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	bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 558.5 260.5 558.5 279.5 801.5 279.5 801.5 260.5 ",
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		pos="680,270",
		rects="558.5,260.5,801.5,279.5",
		width=3.375];
	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 353.5 313.53 365.13 310.78 378.11 307.73 390 305 423.73 297.25 431.77 293.16 466 288 493.17 283.9 522.44 280.76 \
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	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1172 80.5 1172 99.5 1340 99.5 1340 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1256 87.5 0 152 29 -bedGraph to bigwig conversion ",
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		label="bedGraph to bigwig conversion",
		pos="1256,90",
		rects="1172,80.5,1340,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 10 1341.42 316.25 1388.35 309.1 1454 294.84 1454 271 1454 271 1454 271 1454 134 1454 110.46 1399.88 99.78 1348.23 \
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		label=reference_sizes,
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	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 469.19 313.63 492.07 305.99 527.52 294.86 559 288 571.7 285.23 585.26 282.81 598.53 280.74 ",
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	trimming_adapter_trim_end -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 585.18 313.67 589.54 305.83 597.14 294.37 607 288 610.16 285.96 613.54 284.16 617.04 282.58 ",
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		label=adapter_trim_end,
		lp="643,292.5",
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	bisulfite_qc	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 893.5 125.5 893.5 144.5 994.5 144.5 994.5 125.5 ",
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		fillcolor="#F3CEA1",
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		label="Bisulfite QC tools",
		pos="944,135",
		rects="893.5,125.5,994.5,144.5",
		width=1.4028];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 65.66 313.69 73.65 304.14 85 287.63 85 271 85 271 85 271 85 179 85 138.84 691.88 135.81 885.43 135.87 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 885.27 138.32 892.27 135.87 885.28 133.42 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 113.5 223.1 0 57 12 -QCannotation ",
		label=QCannotation,
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		pos="e,893.79,135.87 65.665,313.69 73.647,304.14 85,287.63 85,271 85,271 85,271 85,179 85,138.84 691.88,135.81 885.43,135.87"];
	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 703.94 313.53 696.49 309.6 688.84 304.18 684 297 682.16 294.26 681.03 291 680.37 287.73 ",
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		label=bam,
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	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 839.81 313.55 824.57 310.55 807.03 307.34 791 305 756.08 299.91 744.62 310.47 712 297 710.02 296.18 702.93 290.47 \
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		label=adapter_min_overlap,
		lp="755,292.5",
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	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 1083.18 313.65 1074.73 310.32 1064.54 306.83 1055 305 1000.85 294.61 859.02 315.28 807 297 800.71 294.79 801.15 \
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		label=read_group_id,
		lp="836,292.5",
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	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 1176.51 313.65 1167.34 310.31 1156.29 306.83 1146 305 1116.23 299.72 902.54 306.98 874 297 867.71 294.8 868.22 \
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		label=reference_index,
		lp="907,292.5",
		pos="e,801.12,277.39 1176.5,313.65 1167.3,310.31 1156.3,306.83 1146,305 1116.2,299.72 902.54,306.98 874,297 867.71,294.8 868.22,290.4 \
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	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 13 1174.12 313.53 1165.41 310.53 1155.33 307.32 1146 305 1101.83 293.99 944 316.52 944 271 944 271 944 271 944 179 \
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		label=reference,
		lp="964,225",
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	pileup	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1122.5 170.5 1122.5 189.5 1205.5 189.5 1205.5 170.5 ",
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		height=0.27778,
		label="Biscuit pileup",
		pos="1164,180",
		rects="1122.5,170.5,1205.5,189.5",
		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 4 1195.03 313.6 1189.7 290.82 1174.89 227.55 1167.84 197.39 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1170.24 196.91 1166.26 190.65 1165.47 198.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1200 245.6 0 40 9 -reference ",
		label=reference,
		lp="1200,247.5",
		pos="e,1165.9,189.18 1195,313.6 1189.7,290.82 1174.9,227.55 1167.8,197.39"];
	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1065 125.5 1065 144.5 1447 144.5 1447 125.5 ",
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		height=0.27778,
		label="convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script",
		pos="1256,135",
		rects="1065,125.5,1447,144.5",
		width=5.3056];
	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 1213.93 313.59 1228.43 305.05 1247 290.34 1247 271 1247 271 1247 271 1247 179 1247 170.13 1248.86 160.45 1250.88 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1253.2 153.32 1252.74 145.91 1248.49 151.99 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1267 223.1 0 40 9 -reference ",
		label=reference,
		lp="1267,225",
		pos="e,1253.2,144.46 1213.9,313.59 1228.4,305.05 1247,290.34 1247,271 1247,271 1247,271 1247,179 1247,170.13 1248.9,160.45 1250.9,152.53"];
	bam_to_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 978 170.5 978 189.5 1118 189.5 1118 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1048 177.5 0 124 22 -BAM to CRAM conversion ",
		height=0.27778,
		label="BAM to CRAM conversion",
		pos="1048,180",
		rects="978,170.5,1118,189.5",
		width=1.9444];
	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 7 1189.86 313.69 1169.5 290.03 1111.95 223.43 1102 215 1092.57 207.01 1081.11 199.52 1071.17 193.62 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1155 245.6 0 40 9 -reference ",
		label=reference,
		lp="1155,247.5",
		pos="e,1063.9,189.44 1189.9,313.69 1169.5,290.03 1111.9,223.43 1102,215 1092.6,207.01 1081.1,199.52 1071.2,193.62"];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 210.86 313.51 223.51 310.64 237.85 307.52 251 305 297.86 296.01 309.55 293.04 357 288 420.46 281.26 491.24 277.15 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 550.18 277.13 557.07 274.39 549.98 272.23 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 389 290.6 0 64 14 -min_readlength ",
		label=min_readlength,
		lp="389,292.5",
		pos="e,558.59,274.33 210.86,313.51 223.51,310.64 237.85,307.52 251,305 297.86,296.01 309.55,293.04 357,288 420.46,281.26 491.24,277.15 \
550.33,274.67"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 990 215.5 990 234.5 1100 234.5 1100 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1045 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="1045,225",
		rects="990,215.5,1100,234.5",
		width=1.5278];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 763.93 260.51 823.09 254.32 904.42 245.41 981.66 235.42 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 981.95 237.85 988.58 234.52 981.32 232.99 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 929.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="929.5,247.5",
		pos="e,990.08,234.32 763.93,260.51 823.09,254.32 904.42,245.41 981.66,235.42"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 7 943.68 125.55 943.38 114.9 943.22 96.03 945 80 945.65 74.18 946.81 67.89 948.01 62.31 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 950.32 63.16 949.5 55.79 945.55 62.06 ",
		pos="e,949.84,54.315 943.68,125.55 943.38,114.9 943.22,96.029 945,80 945.65,74.183 946.81,67.885 948.01,62.31"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 7 1125.2 170.56 1100.69 164.35 1072.31 155.24 1065 145 1060.34 138.48 1066.15 89.14 1069.68 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1072.08 63.13 1070.6 55.87 1067.23 62.47 ",
		pos="e,1070.8,54.367 1125.2,170.56 1100.7,164.35 1072.3,155.24 1065,145 1060.3,138.48 1066.2,89.139 1069.7,62.669"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1122.83 170.6 1121.54 170.39 1120.26 170.19 1119 170 1084.54 164.8 1075.27 168.31 1041 162 1020.18 158.17 997.29 \
152.12 978.98 146.83 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 979.77 144.5 972.37 144.88 978.39 149.21 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1047.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="1047.5,157.5",
		pos="e,970.91,144.46 1122.8,170.6 1121.5,170.39 1120.3,170.19 1119,170 1084.5,164.8 1075.3,168.31 1041,162 1020.2,158.17 997.29,152.12 \
978.98,146.83"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 4 1182.18 170.5 1195.91 164.09 1214.95 155.19 1230.25 148.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1231.19 150.3 1236.49 145.12 1229.11 145.86 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1224.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="1224.5,157.5",
		pos="e,1237.9,144.48 1182.2,170.5 1195.9,164.09 1214.9,155.19 1230.2,148.04"];
	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 7 1227.23 125.63 1209.89 119.87 1187.78 111.23 1170 100 1152.53 88.97 1135.59 72.3 1124.58 60.4 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1126.63 59.01 1120.12 55.47 1123 62.3 ",
		pos="e,1119.1,54.344 1227.2,125.63 1209.9,119.87 1187.8,111.23 1170,100 1152.5,88.97 1135.6,72.296 1124.6,60.397"];
	vcf2bed -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 4 1256 125.71 1256 120.59 1256 113.85 1256 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1258.45 107.78 1256 100.78 1253.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1276 110.6 0 40 8 -bedgraph ",
		label=bedgraph,
		lp="1276,112.5",
		pos="e,1256,99.265 1256,125.71 1256,120.59 1256,113.85 1256,107.67"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 945.5 80.5 945.5 99.5 1064.5 99.5 1064.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1005 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="1005,90",
		rects="945.5,80.5,1064.5,99.5",
		width=1.6528];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 1010.01 80.71 1013.32 75.24 1017.76 67.9 1021.7 61.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1023.69 62.82 1025.22 55.56 1019.5 60.28 ",
		pos="e,1026,54.265 1010,80.709 1013.3,75.236 1017.8,67.899 1021.7,61.381"];
	bedgraph_to_bigwig -> cpg_bigwig	[_draw_="c 7 -#000000 B 4 1239.21 80.5 1226.63 74.14 1209.25 65.35 1195.18 58.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1196.46 56.13 1189.11 55.16 1194.25 60.51 ",
		pos="e,1187.8,54.478 1239.2,80.505 1226.6,74.144 1209.3,65.351 1195.2,58.233"];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 4 1043.88 170.56 1036.7 155.87 1021.8 125.39 1012.68 106.71 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1014.99 105.86 1009.71 100.64 1010.58 108.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1040.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="1040.5,135",
		pos="e,1009,99.284 1043.9,170.56 1036.7,155.87 1021.8,125.39 1012.7,106.71"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 999.73 215.54 984.21 210.52 968.01 202.57 957 190 956.68 189.63 951.56 168.11 947.84 152.35 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 950.3 152.08 946.31 145.83 945.53 153.2 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 966.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="966.5,180",
		pos="e,945.96,144.36 999.73,215.54 984.21,210.52 968.01,202.57 957,190 956.68,189.63 951.56,168.11 947.84,152.35"];
	merge -> pileup	[_draw_="c 7 -#000000 B 4 1068.51 215.5 1086.85 208.88 1112.49 199.61 1132.58 192.35 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1133.36 194.68 1139.11 189.99 1131.7 190.07 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1124.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="1124.5,202.5",
		pos="e,1140.5,189.48 1068.5,215.5 1086.8,208.88 1112.5,199.61 1132.6,192.35"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 1045.58 215.71 1045.94 210.59 1046.41 203.85 1046.84 197.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1049.27 197.93 1047.32 190.78 1044.39 197.59 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1055.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="1055.5,202.5",
		pos="e,1047.4,189.27 1045.6,215.71 1045.9,210.59 1046.4,203.85 1046.8,197.67"];
}