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			lp="362,17.5",
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		width=3.375];
	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 1315.72 313.5 1307.55 310.39 1297.95 307.11 1289 305 1225.42 290.01 1208.12 293.2 1143 288 1055.92 281.05 957.69 \
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		label=read_group_id,
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	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 397.5 313.5 406.55 310.39 417.16 307.11 427 305 459.78 297.98 469.38 304.72 502 297 513.09 294.37 514.87 290.45 \
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 559 290.6 0 66 15 -reference_index ",
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	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 7 398.76 313.52 432.57 300.57 495.22 273.3 538 235 550.25 224.04 560.46 208.23 567.04 196.54 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 569.1 197.88 570.27 190.56 564.79 195.56 ",
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		label=reference,
		lp="547,247.5",
		pos="e,570.99,189.23 398.76,313.52 432.57,300.57 495.22,273.3 538,235 550.25,224.04 560.46,208.23 567.04,196.54"];
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		label="Biscuit pileup",
		pos="449,180",
		rects="407.5,170.5,490.5,189.5",
		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 7 377.34 313.86 381.71 299.2 391.88 267.59 405 243 414.14 225.87 427.31 207.95 436.85 195.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 438.59 197.55 441.05 190.56 434.77 194.49 ",
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		label=reference,
		lp="425,247.5",
		pos="e,442,189.38 377.34,313.86 381.71,299.2 391.88,267.59 405,243 414.14,225.87 427.31,207.95 436.85,195.81"];
	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 62 125.5 62 144.5 444 144.5 444 125.5 ",
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		height=0.27778,
		label="convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script",
		pos="253,135",
		rects="62,125.5,444,144.5",
		width=5.3056];
	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 353.37 313.62 336.53 305.51 316 291.44 316 271 316 271 316 271 316 179 316 164.47 304.43 154.5 291.21 147.85 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 292.53 145.75 285.14 145.11 290.51 150.22 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 336 223.1 0 40 9 -reference ",
		label=reference,
		lp="336,225",
		pos="e,283.76,144.49 353.37,313.62 336.53,305.51 316,291.44 316,271 316,271 316,271 316,179 316,164.47 304.43,154.5 291.21,147.85"];
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		fillcolor="#F3CEA1",
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		label="Bisulfite QC tools",
		pos="585,135",
		rects="534.5,125.5,635.5,144.5",
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	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 13 401 313.51 422.52 306.47 449.77 297.53 451 297 472.88 287.45 498 294.87 498 271 498 271 498 271 498 179 498 162.42 \
510.85 152.23 526.68 145.98 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 518 223.1 0 40 9 -reference ",
		label=reference,
		lp="518,225",
		pos="e,534.64,143.21 401,313.51 422.52,306.47 449.77,297.53 451,297 472.88,287.45 498,294.87 498,271 498,271 498,271 498,179 498,162.42 \
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		label=adapter_trim_end,
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	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 508.54 313.57 518.63 310.57 530.28 307.36 541 305 563.84 299.97 570.04 301.41 593 297 610.47 293.65 614.51 291.25 \
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		label=adapters,
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	assay_non_cpg_sites -> vcf2bed	[_draw_="c 7 -#000000 B 10 179.81 313.54 186.91 303.87 197 287.24 197 271 197 271 197 271 197 179 197 165.06 208.04 155.03 220.32 148.17 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 221.12 150.51 226.27 145.18 218.92 146.14 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 240 223.1 0 86 19 -assay_non_cpg_sites ",
		label=assay_non_cpg_sites,
		lp="240,225",
		pos="e,227.62,144.5 179.81,313.54 186.91,303.87 197,287.24 197,271 197,271 197,271 197,179 197,165.06 208.04,155.03 220.32,148.17"];
	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 169 80.5 169 99.5 337 99.5 337 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 253 87.5 0 152 29 -bedGraph to bigwig conversion ",
		height=0.27778,
		label="bedGraph to bigwig conversion",
		pos="253,90",
		rects="169,80.5,337,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 10 60.9 313.76 58.53 303.73 55 286.24 55 271 55 271 55 271 55 134 55 110.46 109.12 99.78 160.77 94.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 160.76 97.41 167.52 94.36 160.33 92.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 87.5 200.6 0 65 15 -reference_sizes ",
		label=reference_sizes,
		lp="87.5,202.5",
		pos="e,169.03,94.223 60.898,313.76 58.528,303.73 55,286.24 55,271 55,271 55,271 55,134 55,110.46 109.12,99.781 160.77,94.949"];
	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 628.38 313.63 645.48 306.4 671.17 295.89 694 288 700.14 285.88 706.69 283.79 713.11 281.84 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 713.66 284.23 719.67 279.89 712.27 279.54 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 722.5 290.6 0 57 12 -max_uncalled ",
		label=max_uncalled,
		lp="722.5,292.5",
		pos="e,721.12,279.46 628.38,313.63 645.48,306.4 671.17,295.89 694,288 700.14,285.88 706.69,283.79 713.11,281.84"];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 752 313.58 752 306.52 752 296.24 752 287.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 754.45 287.78 752 280.78 749.55 287.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 784 290.6 0 64 14 -min_readlength ",
		label=min_readlength,
		lp="784,292.5",
		pos="e,752,279.26 752,313.58 752,306.52 752,296.24 752,287.55"];
	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 891.06 313.63 871.72 306.4 842.69 295.89 817 288 809.79 285.79 802.08 283.61 794.58 281.59 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 886 290.6 0 86 19 -adapter_min_overlap ",
		label=adapter_min_overlap,
		lp="886,292.5",
		pos="e,786.56,279.46 891.06,313.63 871.72,306.4 842.69,295.89 817,288 809.79,285.79 802.08,283.61 794.58,281.59"];
	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 1033.11 313.5 1022.22 310.78 1010.1 307.76 999 305 968.35 297.39 961.14 293.29 930 288 912.35 285 893.62 282.49 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 875.48 277.97 868.26 279.63 874.95 282.84 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 978.5 290.6 0 19 3 -bam ",
		label=bam,
		lp="978.5,292.5",
		pos="e,866.75,279.47 1033.1,313.5 1022.2,310.78 1010.1,307.76 999,305 968.35,297.39 961.14,293.29 930,288 912.35,285 893.62,282.49 875.19,\
280.4"];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1411.08 313.76 1398.19 304.95 1381 289.71 1381 271 1381 271 1381 271 1381 179 1381 142.09 828.07 136.84 643.89 \
136.11 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 643.92 133.66 636.91 136.08 643.9 138.56 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1409.5 223.1 0 57 12 -QCannotation ",
		label=QCannotation,
		lp="1409.5,225",
		pos="e,635.4,136.08 1411.1,313.76 1398.2,304.95 1381,289.71 1381,271 1381,271 1381,271 1381,179 1381,142.09 828.07,136.84 643.89,136.11"];
	bedgraph_to_bigwig -> cpg_bigwig	[_draw_="c 7 -#000000 B 4 272.56 80.5 287.47 74.03 308.2 65.02 324.74 57.84 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 325.65 60.12 331.09 55.08 323.7 55.62 ",
		pos="e,332.48,54.478 272.56,80.505 287.47,74.026 308.2,65.024 324.74,57.84"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 458.5 80.5 458.5 99.5 577.5 99.5 577.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 518 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="518,90",
		rects="458.5,80.5,577.5,99.5",
		width=1.6528];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 512.99 80.71 509.68 75.24 505.24 67.9 501.3 61.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 503.5 60.28 497.78 55.56 499.31 62.82 ",
		pos="e,497,54.265 512.99,80.709 509.68,75.236 505.24,67.899 501.3,61.381"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 580 215.5 580 234.5 690 234.5 690 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 635 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="635,225",
		rects="580,215.5,690,234.5",
		width=1.5278];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 728.88 260.5 710.86 253.88 685.65 244.61 665.89 237.35 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 666.9 235.12 659.49 235 665.21 239.71 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 714.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="714.5,247.5",
		pos="e,658.07,234.48 728.88,260.5 710.86,253.88 685.65,244.61 665.89,237.35"];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 7 505.12 170.84 488.45 168.2 474.67 165.14 472 162 456.26 143.45 480.15 119.18 498.98 104.35 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 500.28 106.44 504.39 100.26 497.33 102.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 486.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="486.5,135",
		pos="e,505.6,99.35 505.12,170.84 488.45,168.2 474.67,165.14 472,162 456.26,143.45 480.15,119.18 498.98,104.35"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 4 449.13 170.68 449.45 149.13 450.32 91.17 450.75 62.51 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 453.2 62.87 450.85 55.83 448.3 62.79 ",
		pos="e,450.87,54.317 449.13,170.68 449.45,149.13 450.32,91.169 450.75,62.509"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 4 410.28 170.5 378.47 163.53 333.31 153.62 299.53 146.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 300.48 143.91 293.12 144.8 299.43 148.7 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 374.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="374.5,157.5",
		pos="e,291.64,144.48 410.28,170.5 378.47,163.53 333.31,153.62 299.53,146.21"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 456.87 170.6 462.9 164.71 471.73 157.16 481 153 495.01 146.71 511.02 142.71 526.2 140.19 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 526.48 142.62 533.04 139.16 525.75 137.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 487.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="487.5,157.5",
		pos="e,534.54,138.93 456.87,170.6 462.9,164.71 471.73,157.16 481,153 495.01,146.71 511.02,142.71 526.2,140.19"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 623.15 215.5 614.76 209.5 603.35 201.32 593.75 194.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 595.18 192.45 588.06 190.36 592.32 196.43 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 619.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="619.5,202.5",
		pos="e,586.83,189.48 623.15,215.5 614.76,209.5 603.35,201.32 593.75,194.43"];
	merge -> pileup	[_draw_="c 7 -#000000 B 4 598.25 215.5 568.19 208.56 525.57 198.7 493.57 191.3 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 494.52 189.01 487.15 189.82 493.41 193.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 567.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="567.5,202.5",
		pos="e,485.67,189.48 598.25,215.5 568.19,208.56 525.57,198.7 493.57,191.3"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 7 639.79 215.72 645.55 204.58 653.45 184.5 645 170 639.38 160.36 629.89 153.23 620.11 148.06 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 621.36 145.94 613.99 145.13 619.24 150.36 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 657.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="657.5,180",
		pos="e,612.62,144.48 639.79,215.72 645.55,204.58 653.45,184.5 645,170 639.38,160.36 629.89,153.23 620.11,148.06"];
	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 7 326.51 125.64 333.66 123.38 340.62 120.55 347 117 371.14 103.56 390.95 77.57 401.85 61.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 403.71 62.68 405.41 55.46 399.58 60.05 ",
		pos="e,406.22,54.187 326.51,125.64 333.66,123.38 340.62,120.55 347,117 371.14,103.56 390.95,77.568 401.85,61.038"];
	vcf2bed -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 4 253 125.71 253 120.59 253 113.85 253 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 255.45 107.78 253 100.78 250.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 299.5 110.6 0 93 20 -methylation_bedgraph ",
		label=methylation_bedgraph,
		lp="299.5,112.5",
		pos="e,253,99.265 253,125.71 253,120.59 253,113.85 253,107.67"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 7 584.1 125.55 582.92 114.9 580.69 96.04 578 80 577.03 74.23 575.79 67.94 574.62 62.36 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 577.09 62.16 573.22 55.83 572.3 63.19 ",
		pos="e,572.9,54.351 584.1,125.55 582.92,114.9 580.69,96.036 578,80 577.03,74.227 575.79,67.941 574.62,62.361"];
}