digraph workflow {
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		cpgs	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1168.5 35.5 1168.5 54.5 1207.5 54.5 1207.5 35.5 ",
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	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1138 125.5 1138 144.5 1520 144.5 1520 125.5 ",
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	assay_non_cpg_sites -> vcf2bed	[_draw_="c 7 -#000000 B 10 1310.05 313.71 1311.24 303.63 1313 286.1 1313 271 1313 271 1313 271 1313 179 1313 169.54 1316.44 159.61 1320.13 \
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	bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 552.5 260.5 552.5 279.5 795.5 279.5 795.5 260.5 ",
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		width=3.375];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 674 313.58 674 306.52 674 296.24 674 287.55 ",
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	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 799.65 313.51 784.05 306.1 760.36 295.4 739 288 732.42 285.72 725.38 283.58 718.45 281.64 ",
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	bisulfite_qc	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 1022.5 125.5 1022.5 144.5 1123.5 144.5 1123.5 125.5 ",
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		label="Bisulfite QC tools",
		pos="1073,135",
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		width=1.4028];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1096.16 313.5 1087.31 304.04 1075 287.85 1075 271 1075 271 1075 271 1075 179 1075 170.3 1074.59 160.62 1074.14 \
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		pos="e,1073.6,144.24 1096.2,313.5 1087.3,304.04 1075,287.85 1075,271 1075,271 1075,271 1075,179 1075,170.3 1074.6,160.62 1074.1,152.65"];
	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 939.8 313.54 908.31 306 860.24 295.08 818 288 801.25 285.19 783.33 282.68 766.02 280.51 ",
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		label=adapter_min_overlap,
		lp="908,292.5",
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	trimming_adapter_trim_end -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 211.11 313.5 239.17 305.42 283.64 293.68 323 288 395.82 277.49 477.92 273.11 544.4 271.42 ",
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		label=adapter_trim_end,
		lp="359,292.5",
		pos="e,552.84,271.21 211.11,313.5 239.17,305.42 283.64,293.68 323,288 395.82,277.49 477.92,273.11 544.4,271.42"];
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		height=0.27778,
		label="Biscuit pileup",
		pos="1147,180",
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		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 7 1198.37 313.69 1198.85 294.97 1198.09 248.51 1181 215 1177.16 207.46 1171.03 200.57 1165.03 194.98 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1166.71 193.2 1159.82 190.46 1163.5 196.9 ",
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		label=reference,
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	bam_to_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 889 170.5 889 189.5 1029 189.5 1029 170.5 ",
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		pos="959,180",
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	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 13 1170.67 313.52 1159.45 309.4 1146.63 303.85 1136 297 1102.44 275.37 1093.06 268.28 1071 235 1061.29 220.35 1070.56 \
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		lp="1102,247.5",
		pos="e,1022,189.48 1170.7,313.52 1159.5,309.4 1146.6,303.85 1136,297 1102.4,275.37 1093.1,268.28 1071,235 1061.3,220.35 1070.6,209.2 \
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	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 1176.99 313.63 1167.91 310.37 1157.08 306.96 1147 305 1090.17 293.98 1074.6 302.75 1017 297 987.98 294.1 981.02 \
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		label=reference_index,
		lp="1050,292.5",
		pos="e,795.26,276.4 1177,313.63 1167.9,310.37 1157.1,306.96 1147,305 1090.2,293.98 1074.6,302.75 1017,297 987.98,294.1 981.02,290.89 \
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	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 13 1191.62 313.72 1180.23 298.66 1156.06 265.52 1140 235 1135.54 226.53 1137.42 222.89 1132 215 1122.74 201.52 1115.28 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1082.94 150.62 1077.58 145.5 1078.58 152.85 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1160 223.1 0 40 9 -reference ",
		label=reference,
		lp="1160,225",
		pos="e,1076.9,144.15 1191.6,313.72 1180.2,298.66 1156.1,265.52 1140,235 1135.5,226.53 1137.4,222.89 1132,215 1122.7,201.52 1115.3,202.72 \
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	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 1217.9 313.65 1234 305.41 1254 291.12 1254 271 1254 271 1254 271 1254 179 1254 163.79 1265.75 153.88 1279.95 147.47 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1274 223.1 0 40 9 -reference ",
		label=reference,
		lp="1274,225",
		pos="e,1287.6,144.42 1217.9,313.65 1234,305.41 1254,291.12 1254,271 1254,271 1254,271 1254,179 1254,163.79 1265.8,153.88 1280,147.47"];
	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 327.31 313.65 335.49 310.55 345.08 307.25 354 305 415.57 289.48 485.54 281.04 544.32 276.45 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 469 290.6 0 58 13 -read_group_id ",
		label=read_group_id,
		lp="469,292.5",
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	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 451.55 313.55 463.03 310.68 476.06 307.56 488 305 530.22 295.95 578.17 287.22 614.8 280.88 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 583.5 290.6 0 19 3 -bam ",
		label=bam,
		lp="583.5,292.5",
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	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 564.63 313.58 586.44 305.09 620.25 291.92 644.51 282.48 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 645.29 284.81 650.93 279.98 643.51 280.24 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 645.5 290.6 0 37 8 -adapters ",
		label=adapters,
		lp="645.5,292.5",
		pos="e,652.34,279.43 564.63,313.58 586.44,305.09 620.25,291.92 644.51,282.48"];
	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1245 80.5 1245 99.5 1413 99.5 1413 80.5 ",
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		height=0.27778,
		label="bedGraph to bigwig conversion",
		pos="1329,90",
		rects="1245,80.5,1413,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 10 1465.43 317.96 1494.7 312.56 1527 300.03 1527 271 1527 271 1527 271 1527 134 1527 110.46 1472.88 99.78 1421.23 \
94.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1421.67 92.53 1414.48 94.36 1421.24 97.41 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1559.5 200.6 0 65 15 -reference_sizes ",
		label=reference_sizes,
		lp="1559.5,202.5",
		pos="e,1413,94.223 1465.4,317.96 1494.7,312.56 1527,300.03 1527,271 1527,271 1527,271 1527,134 1527,110.46 1472.9,99.781 1421.2,94.949"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 7 1144.17 170.74 1141.99 163.93 1139.17 153.96 1138 145 1134.25 116.16 1139.75 82.44 1143.97 62.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1146.34 63.34 1145.49 55.97 1141.56 62.26 ",
		pos="e,1145.8,54.494 1144.2,170.74 1142,163.93 1139.2,153.96 1138,145 1134.2,116.16 1139.8,82.442 1144,62.731"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1129.23 170.53 1124.21 167.96 1118.81 165.01 1114 162 1108.35 158.46 1107.55 156.69 1102 153 1099.76 151.51 1097.4 \
150.01 1095.01 148.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1096.52 146.59 1089.25 145.11 1094 150.8 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1120.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="1120.5,157.5",
		pos="e,1088,144.33 1129.2,170.53 1124.2,167.96 1118.8,165.01 1114,162 1108.4,158.46 1107.6,156.69 1102,153 1099.8,151.51 1097.4,150.01 \
1095,148.55"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 7 1173.6 170.57 1191.42 165.11 1215.47 158.09 1237 153 1247.58 150.5 1258.92 148.15 1269.89 146.03 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1270.29 148.45 1276.71 144.74 1269.38 143.64 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1243.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="1243.5,157.5",
		pos="e,1278.2,144.46 1173.6,170.57 1191.4,165.11 1215.5,158.09 1237,153 1247.6,150.5 1258.9,148.15 1269.9,146.03"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 919.5 80.5 919.5 99.5 1038.5 99.5 1038.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 979 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="979,90",
		rects="919.5,80.5,1038.5,99.5",
		width=1.6528];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 4 960.92 170.56 964.21 156.07 971 126.21 975.26 107.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 977.62 108.13 976.78 100.76 972.84 107.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 980.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="980.5,135",
		pos="e,977.12,99.284 960.92,170.56 964.21,156.07 971,126.21 975.26,107.47"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 926 215.5 926 234.5 1036 234.5 1036 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 981 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="981,225",
		rects="926,215.5,1036,234.5",
		width=1.5278];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 734.65 260.5 787.57 253.09 864.06 242.38 917.73 234.86 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 918.05 237.29 924.64 233.89 917.37 232.44 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 865.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="865.5,247.5",
		pos="e,926.14,233.68 734.65,260.5 787.57,253.09 864.06,242.38 917.73,234.86"];
	bedgraph_to_bigwig -> cpg_bigwig	[_draw_="c 7 -#000000 B 4 1312.8 80.5 1300.67 74.14 1283.9 65.35 1270.33 58.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1271.84 56.26 1264.51 55.18 1269.57 60.6 ",
		pos="e,1263.2,54.478 1312.8,80.505 1300.7,74.144 1283.9,65.351 1270.3,58.233"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 4 1073 125.56 1073 111.14 1073 81.48 1073 62.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1075.45 62.8 1073 55.8 1070.55 62.8 ",
		pos="e,1073,54.284 1073,125.56 1073,111.14 1073,81.476 1073,62.727"];
	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 7 1299.33 125.53 1282.07 119.83 1260.37 111.29 1243 100 1226.31 89.15 1210.44 72.67 1200.07 60.77 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1202.02 59.28 1195.62 55.52 1198.28 62.45 ",
		pos="e,1194.6,54.369 1299.3,125.53 1282.1,119.83 1260.4,111.29 1243,100 1226.3,89.149 1210.4,72.669 1200.1,60.769"];
	vcf2bed -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 4 1329 125.71 1329 120.59 1329 113.85 1329 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1331.45 107.78 1329 100.78 1326.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1375.5 110.6 0 93 20 -methylation_bedgraph ",
		label=methylation_bedgraph,
		lp="1375.5,112.5",
		pos="e,1329,99.265 1329,125.71 1329,120.59 1329,113.85 1329,107.67"];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 981.89 80.71 983.72 75.47 986.14 68.53 988.34 62.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 990.63 63.11 990.62 55.69 986 61.5 ",
		pos="e,991.12,54.265 981.89,80.709 983.72,75.474 986.14,68.534 988.34,62.235"];
	merge -> pileup	[_draw_="c 7 -#000000 B 4 1013.8 215.5 1040.28 208.64 1077.7 198.95 1106.13 191.59 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1106.64 193.98 1112.81 189.86 1105.42 189.24 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1087.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="1087.5,202.5",
		pos="e,1114.3,189.48 1013.8,215.5 1040.3,208.64 1077.7,198.95 1106.1,191.59"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 976.76 215.71 974.02 210.36 970.37 203.22 967.09 196.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 969.29 195.73 963.92 190.61 964.93 197.96 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 980.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="980.5,202.5",
		pos="e,963.23,189.27 976.76,215.71 974.02,210.36 970.37,203.22 967.09,196.81"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 994.78 215.67 1004.8 209.28 1018.41 199.9 1029 190 1041.75 178.08 1054.12 162.43 1062.47 151.05 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1064.37 152.61 1066.47 145.5 1060.39 149.75 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1056.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="1056.5,180",
		pos="e,1067.4,144.27 994.78,215.67 1004.8,209.28 1018.4,199.9 1029,190 1041.8,178.08 1054.1,162.43 1062.5,151.05"];
}