digraph workflow {
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			width=1.875];
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			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 238 320.5 0 70 11 -sample_name ",
			fillcolor="#94DDF4",
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			rects="195,313.5,281,332.5",
			width=1.1944];
		reference_index	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 95.5 313.5 95.5 332.5 190.5 332.5 190.5 313.5 ",
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			rects="95.5,313.5,190.5,332.5",
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	subgraph cluster_outputs {
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			lwidth=1.28,
			rank=same,
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			rects="429.5,35.5,500.5,54.5",
			width=0.98611];
		vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 393 35.5 393 54.5 425 54.5 425 35.5 ",
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			fillcolor="#94DDF4",
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			rects="393,35.5,425,54.5",
			width=0.44444];
		gathered_directory	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 504.5 35.5 504.5 54.5 613.5 54.5 613.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 559 42.5 0 93 18 -gathered_directory ",
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			width=1.5139];
		cpgs	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 349.5 35.5 349.5 54.5 388.5 54.5 388.5 35.5 ",
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			width=0.56944];
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	bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 458.5 260.5 458.5 279.5 701.5 279.5 701.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 580 267.5 0 227 44 -bam to trimmed fastqs and biscuit alignments ",
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		pos="580,270",
		rects="458.5,260.5,701.5,279.5",
		width=3.375];
	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 349.34 313.63 357.32 310.68 366.5 307.48 375 305 413.32 293.83 456.8 285.97 493.83 280.64 ",
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		label=read_group_id,
		lp="476,292.5",
		pos="e,502.12,279.47 349.34,313.63 357.32,310.68 366.5,307.48 375,305 413.32,293.83 456.8,285.97 493.83,280.64"];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 580 313.58 580 306.52 580 296.24 580 287.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 582.45 287.78 580 280.78 577.55 287.78 ",
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		label=min_readlength,
		lp="612,292.5",
		pos="e,580,279.26 580,313.58 580,306.52 580,296.24 580,287.55"];
	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 821.06 313.56 790.36 306.13 743.85 295.38 703 288 688.23 285.33 672.4 282.86 657.18 280.67 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 787 290.6 0 86 19 -adapter_min_overlap ",
		label=adapter_min_overlap,
		lp="787,292.5",
		pos="e,648.79,279.49 821.06,313.56 790.36,306.13 743.85,295.38 703,288 688.23,285.33 672.4,282.86 657.18,280.67"];
	bisulfite_qc	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 496.5 125.5 496.5 144.5 597.5 144.5 597.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 547 132.5 0 85 18 -Bisulfite QC tools ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="Bisulfite QC tools",
		pos="547,135",
		rects="496.5,125.5,597.5,144.5",
		width=1.4028];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1366.78 313.79 1355.02 304.81 1339 289.23 1339 271 1339 271 1339 271 1339 179 1339 139.61 696.1 148.46 605.55 \
144.97 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 605.97 142.54 598.83 144.56 605.67 147.43 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1367.5 223.1 0 57 12 -QCannotation ",
		label=QCannotation,
		lp="1367.5,225",
		pos="e,597.32,144.47 1366.8,313.79 1355,304.81 1339,289.23 1339,271 1339,271 1339,271 1339,179 1339,139.61 696.1,148.46 605.55,144.97"];
	trimming_adapter_trim_end -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 1123.07 313.55 1109.56 310.62 1094.13 307.46 1080 305 955.46 283.33 811.23 275.31 709.78 272.42 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 709.9 269.97 702.84 272.23 709.77 274.87 ",
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		label=adapter_trim_end,
		lp="1062,292.5",
		pos="e,701.32,272.19 1123.1,313.55 1109.6,310.62 1094.1,307.46 1080,305 955.46,283.33 811.23,275.31 709.78,272.42"];
	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 396 80.5 396 99.5 564 99.5 564 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 480 87.5 0 152 29 -bedGraph to bigwig conversion ",
		height=0.27778,
		label="bedGraph to bigwig conversion",
		pos="480,90",
		rects="396,80.5,564,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 13 1264.66 313.56 1247.6 305.49 1227 291.51 1227 271 1227 271 1227 271 1227 134 1227 97.84 613.07 102.62 577 100 \
575.39 99.88 573.76 99.76 572.12 99.64 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 572.52 97.21 565.35 99.11 572.14 102.1 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1259.5 200.6 0 65 15 -reference_sizes ",
		label=reference_sizes,
		lp="1259.5,202.5",
		pos="e,563.84,98.991 1264.7,313.56 1247.6,305.49 1227,291.51 1227,271 1227,271 1227,271 1227,134 1227,97.84 613.07,102.62 577,100 575.39,\
99.883 573.76,99.762 572.12,99.638"];
	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 463.12 313.58 486.63 305.01 523.19 291.7 549.16 282.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 549.69 284.65 555.43 279.95 548.01 280.05 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 539.5 290.6 0 19 3 -bam ",
		label=bam,
		lp="539.5,292.5",
		pos="e,556.85,279.43 463.12,313.58 486.63,305.01 523.19,291.7 549.16,282.24"];
	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 697 313.64 683.92 306.1 663.66 295.15 645 288 638.95 285.68 632.46 283.57 626.02 281.68 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 626.77 279.35 619.37 279.82 625.45 284.07 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 683.5 290.6 0 37 8 -adapters ",
		label=adapters,
		lp="683.5,292.5",
		pos="e,617.91,279.42 697,313.64 683.92,306.1 663.66,295.15 645,288 638.95,285.68 632.46,283.57 626.02,281.68"];
	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 979.25 313.57 967.26 310.64 953.56 307.47 941 305 892.46 295.45 880.17 293.45 831 288 791.69 283.64 748.78 280.24 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 710.12 275.23 702.98 277.22 709.81 280.12 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 925.5 290.6 0 57 12 -max_uncalled ",
		label=max_uncalled,
		lp="925.5,292.5",
		pos="e,701.47,277.12 979.25,313.57 967.26,310.64 953.56,307.47 941,305 892.46,295.45 880.17,293.45 831,288 791.69,283.64 748.78,280.24 \
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	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 0 125.5 0 144.5 382 144.5 382 125.5 ",
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		height=0.27778,
		label="convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script",
		pos="191,135",
		rects="0,125.5,382,144.5",
		width=5.3056];
	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 158.98 313.58 172.95 304.95 191 290.09 191 271 191 271 191 271 191 179 191 170.31 191 160.63 191 152.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 193.45 152.76 191 145.76 188.55 152.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 211 223.1 0 40 9 -reference ",
		label=reference,
		lp="211,225",
		pos="e,191,144.24 158.98,313.58 172.95,304.95 191,290.09 191,271 191,271 191,271 191,179 191,170.31 191,160.63 191,152.65"];
	bam_to_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 469 170.5 469 189.5 609 189.5 609 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 539 177.5 0 124 22 -BAM to CRAM conversion ",
		height=0.27778,
		label="BAM to CRAM conversion",
		pos="539,180",
		rects="469,170.5,609,189.5",
		width=1.9444];
	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 7 163.69 313.63 230.81 286.49 439.06 202.43 454 198 462.51 195.48 471.6 193.21 480.56 191.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 480.93 193.65 487.26 189.79 479.9 188.86 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 356 245.6 0 40 9 -reference ",
		label=reference,
		lp="356,247.5",
		pos="e,488.74,189.48 163.69,313.63 230.81,286.49 439.06,202.43 454,198 462.51,195.48 471.6,193.21 480.56,191.23"];
	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 164.96 313.52 174.11 310.33 184.94 306.99 195 305 241.34 295.82 254.29 304.11 301 297 318.59 294.32 322.41 290.64 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 450.41 278.92 457.22 276 450.07 274.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 373 290.6 0 66 15 -reference_index ",
		label=reference_index,
		lp="373,292.5",
		pos="e,458.73,275.9 164.96,313.52 174.11,310.33 184.94,306.99 195,305 241.34,295.82 254.29,304.11 301,297 318.59,294.32 322.41,290.64 \
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	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 13 143 313.7 143 303.6 143 286.05 143 271 143 271 143 271 143 179 143 120.95 213.45 160.58 271 153 291.85 150.25 \
413.49 143.3 488.16 139.19 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 488.21 141.64 495.06 138.81 487.94 136.75 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 163 223.1 0 40 9 -reference ",
		label=reference,
		lp="163,225",
		pos="e,496.58,138.73 143,313.7 143,303.6 143,286.05 143,271 143,271 143,271 143,179 143,120.95 213.45,160.58 271,153 291.85,150.25 413.49,\
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		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 389 177.5 0 67 14 -Biscuit pileup ",
		height=0.27778,
		label="Biscuit pileup",
		pos="389,180",
		rects="347.5,170.5,430.5,189.5",
		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 10 164.67 313.58 174.37 309.31 185.7 303.63 195 297 245.41 261.06 238.17 226.75 293 198 307.04 190.64 323.66 186.39 \
339.08 183.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 339.41 186.39 346.01 183 338.74 181.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 263 245.6 0 40 9 -reference ",
		label=reference,
		lp="263,247.5",
		pos="e,347.51,182.79 164.67,313.58 174.37,309.31 185.7,303.63 195,297 245.41,261.06 238.17,226.75 293,198 307.04,190.64 323.66,186.39 \
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	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 4 208.07 125.56 239.83 109.86 308.11 76.1 344.68 58.02 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 345.44 60.38 350.63 55.08 343.27 55.99 ",
		pos="e,351.98,54.412 208.07,125.56 239.83,109.86 308.11,76.105 344.68,58.021"];
	vcf2bed -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 4 248.1 125.5 296.09 118.36 364.69 108.16 414.83 100.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 414.96 103.15 421.52 99.7 414.24 98.31 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 381 110.6 0 40 8 -bedgraph ",
		label=bedgraph,
		lp="381,112.5",
		pos="e,423.02,99.478 248.1,125.5 296.09,118.36 364.69,108.16 414.83,100.7"];
	bedgraph_to_bigwig -> cpg_bigwig	[_draw_="c 7 -#000000 B 4 477.11 80.71 475.28 75.47 472.86 68.53 470.66 62.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 473 61.5 468.38 55.69 468.37 63.11 ",
		pos="e,467.88,54.265 477.11,80.709 475.28,75.474 472.86,68.534 470.66,62.235"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 578.5 80.5 578.5 99.5 697.5 99.5 697.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 638 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="638,90",
		rects="578.5,80.5,697.5,99.5",
		width=1.6528];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 7 558.1 170.51 570.33 164.49 586.09 155.62 598 145 610.6 133.77 621.73 118 629.03 106.39 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 631.11 107.68 632.65 100.43 626.92 105.14 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 625.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="625.5,135",
		pos="e,633.44,99.136 558.1,170.51 570.33,164.49 586.09,155.62 598,145 610.6,133.77 621.73,118 629.03,106.39"];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 638 80.71 638 75.59 638 68.85 638 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 640.45 62.78 638 55.78 635.55 62.78 ",
		pos="e,638,54.265 638,80.709 638,75.593 638,68.848 638,62.666"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 496 215.5 496 234.5 606 234.5 606 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 551 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="551,225",
		rects="496,215.5,606,234.5",
		width=1.5278];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 574.41 260.71 570.64 255.12 565.55 247.58 561.09 240.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 563.37 239.95 557.42 235.52 559.3 242.69 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 579.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="579.5,247.5",
		pos="e,556.57,234.27 574.41,260.71 570.64,255.12 565.55,247.58 561.09,240.96"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 7 552.49 125.76 556.57 119.12 561.79 109.38 564 100 566.94 87.54 565.35 73.09 563.21 62.27 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 565.64 61.92 561.7 55.64 560.86 63.01 ",
		pos="e,561.37,54.164 552.49,125.76 556.57,119.12 561.79,109.38 564,100 566.94,87.544 565.35,73.09 563.21,62.272"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 7 388.77 170.67 388.47 153.49 388.7 112.97 396 80 397.34 73.95 399.56 67.54 401.79 61.94 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 403.9 63.24 404.38 55.84 399.39 61.33 ",
		pos="e,404.97,54.448 388.77,170.67 388.47,153.49 388.7,112.97 396,80 397.34,73.948 399.56,67.541 401.79,61.941"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 4 349.88 170.5 317.75 163.53 272.13 153.62 238.01 146.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 238.88 143.89 231.52 144.8 237.84 148.68 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 313.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="313.5,157.5",
		pos="e,230.04,144.48 349.88,170.5 317.75,163.53 272.13,153.62 238.01,146.21"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 4 420.22 170.5 445.32 163.67 480.73 154.03 507.75 146.68 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 508.28 149.08 514.39 144.88 506.99 144.35 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 488.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="488.5,157.5",
		pos="e,515.85,144.48 420.22,170.5 445.32,163.67 480.73,154.03 507.75,146.68"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 548.69 215.71 547.23 210.47 545.29 203.53 543.53 197.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 545.95 196.81 541.71 190.72 541.24 198.12 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 555.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="555.5,202.5",
		pos="e,541.31,189.27 548.69,215.71 547.23,210.47 545.29,203.53 543.53,197.24"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 577.12 215.56 589.08 210.25 602.09 202.05 609 190 613.42 182.29 613.53 177.65 609 170 603.22 160.24 593.53 153.09 \
583.51 147.94 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 584.59 145.75 577.21 145.03 582.53 150.19 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 621.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="621.5,180",
		pos="e,575.84,144.39 577.12,215.56 589.08,210.25 602.09,202.05 609,190 613.42,182.29 613.53,177.65 609,170 603.22,160.24 593.53,153.09 \
583.51,147.94"];
	merge -> pileup	[_draw_="c 7 -#000000 B 4 518.99 215.5 493.14 208.64 456.63 198.95 428.88 191.59 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 429.8 189.29 422.4 189.87 428.54 194.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 493.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="493.5,202.5",
		pos="e,420.94,189.48 518.99,215.5 493.14,208.64 456.63,198.95 428.88,191.59"];
}