digraph workflow {
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		output_picard_mark_duplicates_files	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1122.5 35.5 1122.5 54.5 1317.5 54.5 1317.5 35.5 ",
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		output_percent_mitochondrial_reads	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 284.5 35.5 284.5 54.5 479.5 54.5 479.5 35.5 ",
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	"bowtie-se"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 600.5 665.5 600.5 684.5 665.5 684.5 665.5 665.5 ",
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	nthreads -> "bowtie-se"	[_draw_="c 7 -#000000 B 13 829.3 718.67 823.53 715.5 816.62 712.14 810 710 787.33 702.67 778.97 711.2 757 702 750.85 699.42 751.15 695.58 \
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	sort_dedup_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 723.5 125.5 723.5 144.5 826.5 144.5 826.5 125.5 ",
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	nthreads -> sort_dedup_bams	[_draw_="c 7 -#000000 B 10 831.3 718.69 811.61 703.63 774 669.79 774 631 774 631 774 631 774 179 774 170.31 774.21 160.62 774.43 152.65 ",
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	sam2bam	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 826.5 620.5 826.5 639.5 891.5 639.5 891.5 620.5 ",
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	nthreads -> sam2bam	[_draw_="c 7 -#000000 B 7 842.58 718.87 842.15 706.92 842.02 683.98 846 665 847.27 658.93 849.48 652.52 851.72 646.92 ",
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		label=sort_bams,
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	nthreads -> sort_bams	[_draw_="c 7 -#000000 B 10 852.58 718.59 860.98 710.71 872.94 698.19 880 685 888.69 668.76 897.57 620.55 892 603 891.88 602.62 891.75 602.24 \
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	sort_masked_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 966.5 395.5 966.5 414.5 1077.5 414.5 1077.5 395.5 ",
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		width=1.5417];
	nthreads -> sort_masked_bams	[_draw_="c 7 -#000000 B 19 859.81 718.64 879.77 707.65 911.98 686.24 925 657 933.82 637.19 973.36 677.85 915 575 912.19 570.05 908.2 571.71 \
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		height=0.27778,
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	nthreads -> filtered2sorted	[_draw_="c 7 -#000000 B 16 857.12 718.63 863.07 715.45 870.19 712.1 877 710 926.71 694.67 989 728.02 989 676 989 676 989 676 989 584 989 \
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1007.5 605.6 0 37 8 -nthreads ",
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		label=sort_dups_marked_bams,
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	nthreads -> sort_dups_marked_bams	[_draw_="c 7 -#000000 B 10 840.15 718.78 833.8 699.68 819 650.69 819 608.5 819 608.5 819 608.5 819 314 819 296.25 857.44 285.5 895.91 279.19 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 896.07 281.64 902.61 278.14 895.32 276.8 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 837.5 493.1 0 37 8 -nthreads ",
		label=nthreads,
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		pos="e,904.11,277.91 840.15,718.78 833.8,699.68 819,650.69 819,608.5 819,608.5 819,608.5 819,314 819,296.25 857.44,285.5 895.91,279.19"];
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		label=remove_encode_blacklist,
		pos="1168,450",
		rects="1097.5,440.5,1238.5,459.5",
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	ENCODE_blacklist_bedfile -> remove_encode_blacklist	[_draw_="c 7 -#000000 B 10 1102.65 718.55 1125.38 711.58 1147 698.93 1147 676 1147 676 1147 676 1147 494 1147 483.95 1151.69 473.8 1156.64 \
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	input_fastq_files -> "bowtie-se"	[_draw_="c 7 -#000000 B 7 582.74 718.62 569.83 712.28 557.21 702.98 565 693 568.78 688.16 580.14 684.5 592.52 681.83 ",
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		label=input_fastq_file,
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	input_fastq_files -> extract_basename_1	[_draw_="c 7 -#000000 B 7 612.97 737.2 622.92 745.77 639.85 758.8 657 765 706.93 783.06 851.11 792.31 937.42 796.36 ",
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		label=input_file,
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	execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 1291 440.5 1291 459.5 1449 459.5 1449 440.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1370 447.5 0 142 27 -execute_pcr_bottleneck_coef ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label=execute_pcr_bottleneck_coef,
		pos="1370,450",
		rects="1291,440.5,1449,459.5",
		width=2.1944];
	genome_sizes_file -> execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 B 13 1277 718.7 1277 708.6 1277 691.05 1277 676 1277 676 1277 676 1277 606.5 1277 592.44 1275.03 588.15 1280 575 1296.96 \
530.13 1334.69 486.94 1355.51 465.33 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1357.17 467.13 1360.33 460.42 1353.67 463.7 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1309.5 583.1 0 59 12 -genome_sizes ",
		label=genome_sizes,
		lp="1309.5,585",
		pos="e,1361.4,459.34 1277,718.7 1277,708.6 1277,691.05 1277,676 1277,676 1277,676 1277,606.5 1277,592.44 1275,588.15 1280,575 1297,530.13 \
1334.7,486.94 1355.5,465.33"];
	mark_duplicates	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1058 305.5 1058 324.5 1156 324.5 1156 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1107 312.5 0 82 15 -mark_duplicates ",
		height=0.27778,
		label=mark_duplicates,
		pos="1107,315",
		rects="1058,305.5,1156,324.5",
		width=1.3611];
	picard_java_opts -> mark_duplicates	[_draw_="c 7 -#000000 B 16 948.83 718.55 958.34 715.36 969.58 712.02 980 710 1002.54 705.64 1065.33 716.66 1083 702 1092.21 694.36 1090 687.97 \
1090 676 1090 676 1090 676 1090 449 1090 406.71 1098.56 357.45 1103.53 332.42 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1105.88 333.19 1104.88 325.84 1101.08 332.21 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1110 515.6 0 40 9 -java_opts ",
		label=java_opts,
		lp="1110,517.5",
		pos="e,1105.2,324.36 948.83,718.55 958.34,715.36 969.58,712.02 980,710 1002.5,705.64 1065.3,716.66 1083,702 1092.2,694.36 1090,687.97 \
1090,676 1090,676 1090,676 1090,449 1090,406.71 1098.6,357.45 1103.5,332.42"];
	genome_ref_first_index_file -> "bowtie-se"	[_draw_="c 7 -#000000 B 7 692.08 718.54 667.77 713.13 640.92 706.35 637 702 634.66 699.4 633.36 696.04 632.69 692.59 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 635.14 692.57 632.19 685.76 630.26 692.92 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 692.5 695.6 0 111 27 -genome_ref_first_index_file ",
		label=genome_ref_first_index_file,
		lp="692.5,697.5",
		pos="e,632.08,684.25 692.08,718.54 667.77,713.13 640.92,706.35 637,702 634.66,699.4 633.36,696.04 632.69,692.59"];
	picard_jar_path -> mark_duplicates	[_draw_="c 7 -#000000 B 16 1202.29 718.65 1221.85 711.07 1244 697.7 1244 676 1244 676 1244 676 1244 494 1244 464.88 1246 457.62 1246 428.5 \
1246 428.5 1246 428.5 1246 359 1246 340.84 1202.16 329.52 1163.72 323.08 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1164.41 320.71 1157.11 322.02 1163.63 325.54 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1275.5 515.6 0 63 15 -picard_jar_path ",
		label=picard_jar_path,
		lp="1275.5,517.5",
		pos="e,1155.6,321.78 1202.3,718.65 1221.8,711.07 1244,697.7 1244,676 1244,676 1244,676 1244,494 1244,464.88 1246,457.62 1246,428.5 1246,\
428.5 1246,428.5 1246,359 1246,340.84 1202.2,329.52 1163.7,323.08"];
	"bowtie-se" -> output_bowtie_log	[_draw_="c 7 -#000000 B 10 600.53 673.18 482.21 669.99 81 657.22 81 631 81 631 81 631 81 89 81 80.04 78.73 70.35 76.26 62.44 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 78.57 61.65 73.97 55.83 73.94 63.25 ",
		pos="e,73.48,54.404 600.53,673.18 482.21,669.99 81,657.22 81,631 81,631 81,631 81,89 81,80.042 78.732,70.353 76.255,62.444"];
	"bowtie-se" -> sam2bam	[_draw_="c 7 -#000000 B 4 665.38 667.84 705.74 660.16 774.74 647.03 818.54 638.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 818.77 641.15 825.19 637.43 817.86 636.33 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 785 650.6 0 38 10 -input_file ",
		label=input_file,
		lp="785,652.5",
		pos="e,826.68,637.15 665.38,667.84 705.74,660.16 774.74,647.03 818.54,638.7"];
	mapped_reads_count	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 185.5 80.5 185.5 99.5 306.5 99.5 306.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 246 87.5 0 105 18 -mapped_reads_count ",
		height=0.27778,
		label=mapped_reads_count,
		pos="246,90",
		rects="185.5,80.5,306.5,99.5",
		width=1.6806];
	"bowtie-se" -> mapped_reads_count	[_draw_="c 7 -#000000 B 10 600.61 672.28 551.79 668.79 465 658.7 465 631 465 631 465 631 465 134 465 118.44 378.78 105.48 314.54 97.98 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 315.16 95.58 307.93 97.22 314.6 100.45 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 487.5 380.6 0 45 10 -bowtie_log ",
		label=bowtie_log,
		lp="487.5,382.5",
		pos="e,306.42,97.047 600.61,672.28 551.79,668.79 465,658.7 465,631 465,631 465,631 465,134 465,118.44 378.78,105.48 314.54,97.978"];
	index_dedup_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 721.5 80.5 721.5 99.5 832.5 99.5 832.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 777 87.5 0 95 16 -index_dedup_bams ",
		height=0.27778,
		label=index_dedup_bams,
		pos="777,90",
		rects="721.5,80.5,832.5,99.5",
		width=1.5417];
	index_dedup_bams -> output_data_sorted_dedup_bam_files	[_draw_="c 7 -#000000 B 4 777.58 80.71 777.94 75.59 778.41 68.85 778.84 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 781.27 62.93 779.32 55.78 776.39 62.59 ",
		pos="e,779.42,54.265 777.58,80.709 777.94,75.593 778.41,68.848 778.84,62.666"];
	extract_basename_2	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1347.5 718.5 1347.5 737.5 1466.5 737.5 1466.5 718.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1407 725.5 0 103 18 -extract_basename_2 ",
		height=0.27778,
		label=extract_basename_2,
		pos="1407,728",
		rects="1347.5,718.5,1466.5,737.5",
		width=1.6528];
	extract_basename_1 -> extract_basename_2	[_draw_="c 7 -#000000 B 7 1064.47 799.89 1132.53 799.34 1246.65 793.58 1340 765 1357.1 759.77 1374.86 749.99 1387.79 741.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1388.96 744.12 1393.53 738.28 1386.32 739.99 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1322 775.6 0 36 9 -file_path ",
		label=file_path,
		lp="1322,777.5",
		pos="e,1394.8,737.46 1064.5,799.89 1132.5,799.34 1246.7,793.58 1340,765 1357.1,759.77 1374.9,749.99 1387.8,741.95"];
	bam_idxstats	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 543.5 125.5 543.5 144.5 626.5 144.5 626.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 585 132.5 0 67 12 -bam_idxstats ",
		height=0.27778,
		label=bam_idxstats,
		pos="585,135",
		rects="543.5,125.5,626.5,144.5",
		width=1.1528];
	percent_mitochondrial_reads	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 359 80.5 359 99.5 517 99.5 517 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 438 87.5 0 142 27 -percent_mitochondrial_reads ",
		height=0.27778,
		label=percent_mitochondrial_reads,
		pos="438,90",
		rects="359,80.5,517,99.5",
		width=2.1944];
	bam_idxstats -> percent_mitochondrial_reads	[_draw_="c 7 -#000000 B 4 555.96 125.5 532.7 118.7 499.94 109.12 474.84 101.78 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 475.84 99.52 468.43 99.9 474.47 104.22 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 540.5 110.6 0 33 8 -idxstats ",
		label=idxstats,
		lp="540.5,112.5",
		pos="e,466.98,99.478 555.96,125.5 532.7,118.7 499.94,109.12 474.84,101.78"];
	remove_encode_blacklist -> sort_masked_bams	[_draw_="c 7 -#000000 B 4 1139.16 440.5 1116.16 433.73 1083.8 424.2 1058.91 416.87 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1059.64 414.53 1052.24 414.91 1058.26 419.23 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1127 425.6 0 38 10 -input_file ",
		label=input_file,
		lp="1127,427.5",
		pos="e,1050.8,414.48 1139.2,440.5 1116.2,433.73 1083.8,424.2 1058.9,416.87"];
	masked_file_basename	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1096.5 395.5 1096.5 414.5 1227.5 414.5 1227.5 395.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1162 402.5 0 115 20 -masked_file_basename ",
		height=0.27778,
		label=masked_file_basename,
		pos="1162,405",
		rects="1096.5,395.5,1227.5,414.5",
		width=1.8194];
	remove_encode_blacklist -> masked_file_basename	[_draw_="c 7 -#000000 B 4 1166.84 440.71 1166.13 435.59 1165.19 428.85 1164.33 422.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1166.76 422.36 1163.36 415.76 1161.9 423.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1184 425.6 0 38 10 -input_file ",
		label=input_file,
		lp="1184,427.5",
		pos="e,1163.2,414.27 1166.8,440.71 1166.1,435.59 1165.2,428.85 1164.3,422.67"];
	percent_mitochondrial_reads -> output_percent_mitochondrial_reads	[_draw_="c 7 -#000000 B 4 426.94 80.5 419.19 74.56 408.67 66.48 399.76 59.64 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 401.29 57.72 394.24 55.4 398.3 61.61 ",
		pos="e,393.04,54.478 426.94,80.505 419.19,74.556 408.67,66.481 399.76,59.637"];
	sort_dedup_bams -> index_dedup_bams	[_draw_="c 7 -#000000 B 4 775.39 125.71 775.62 120.59 775.94 113.85 776.22 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 778.67 107.88 776.55 100.78 773.77 107.66 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 795 110.6 0 38 10 -input_file ",
		label=input_file,
		lp="795,112.5",
		pos="e,776.62,99.265 775.39,125.71 775.62,120.59 775.94,113.85 776.22,107.67"];
	mapped_filtered_reads_count	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 544.5 80.5 544.5 99.5 705.5 99.5 705.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 625 87.5 0 145 27 -mapped_filtered_reads_count ",
		height=0.27778,
		label=mapped_filtered_reads_count,
		pos="625,90",
		rects="544.5,80.5,705.5,99.5",
		width=2.2361];
	sort_dedup_bams -> mapped_filtered_reads_count	[_draw_="c 7 -#000000 B 7 744.26 125.51 734.57 122.82 723.83 119.81 714 117 696.73 112.07 677.61 106.5 661.54 101.78 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 662.29 99.45 654.88 99.83 660.91 104.15 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 744 110.6 0 60 14 -input_bam_file ",
		label=input_bam_file,
		lp="744,112.5",
		pos="e,653.43,99.404 744.26,125.51 734.57,122.82 723.83,119.81 714,117 696.73,112.07 677.61,106.5 661.54,101.78"];
	sam2bam -> sort_bams	[_draw_="c 7 -#000000 B 7 856.27 620.84 854.97 615.49 854.23 608.5 857 603 857.48 602.05 858.04 601.14 858.66 600.28 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 860.2 602.2 863.34 595.48 856.7 598.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 876 605.6 0 38 10 -input_file ",
		label=input_file,
		lp="876,607.5",
		pos="e,864.4,594.4 856.27,620.84 854.97,615.49 854.23,608.5 857,603 857.48,602.05 858.04,601.14 858.66,600.28"];
	mapped_reads_count -> output_read_count_mapped	[_draw_="c 7 -#000000 B 4 237.9 80.71 232.21 74.88 224.45 66.93 217.79 60.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 219.77 58.64 213.13 55.35 216.27 62.07 ",
		pos="e,212.07,54.265 237.9,80.709 232.21,74.879 224.45,66.934 217.79,60.117"];
	remove_duplicates	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 863 170.5 863 189.5 973 189.5 973 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 918 177.5 0 94 17 -remove_duplicates ",
		height=0.27778,
		label=remove_duplicates,
		pos="918,180",
		rects="863,170.5,973,189.5",
		width=1.5278];
	remove_duplicates -> sort_dedup_bams	[_draw_="c 7 -#000000 B 4 889.75 170.5 867.22 163.73 835.53 154.2 811.15 146.87 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 812.05 144.58 804.64 144.91 810.64 149.28 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 878 155.6 0 38 10 -input_file ",
		label=input_file,
		lp="878,157.5",
		pos="e,803.19,144.48 889.75,170.5 867.22,163.73 835.53,154.2 811.15,146.87"];
	"filter-unmapped"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 987.5 530.5 987.5 549.5 1082.5 549.5 1082.5 530.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1035 537.5 0 79 15 -filter-unmapped ",
		height=0.27778,
		label="filter-unmapped",
		pos="1035,540",
		rects="987.5,530.5,1082.5,549.5",
		width=1.3194];
	sort_bams -> "filter-unmapped"	[_draw_="c 7 -#000000 B 4 910.62 575.5 935.25 568.67 969.99 559.03 996.5 551.68 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 996.89 554.11 1002.98 549.88 995.58 549.39 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 990 560.6 0 38 10 -input_file ",
		label=input_file,
		lp="990,562.5",
		pos="e,1004.4,549.48 910.62,575.5 935.25,568.67 969.99,559.03 996.5,551.68"];
	index_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 782 170.5 782 189.5 858 189.5 858 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 820 177.5 0 60 10 -index_bams ",
		height=0.27778,
		label=index_bams,
		pos="820,180",
		rects="782,170.5,858,189.5",
		width=1.0556];
	sort_bams -> index_bams	[_draw_="c 7 -#000000 B 10 875.57 575.69 871.47 567.22 866 553.56 866 541 866 541 866 541 866 224 866 211.09 856.21 200.94 845.66 193.75 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 847.24 191.84 840 190.25 844.66 196.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 885 380.6 0 38 10 -input_file ",
		label=input_file,
		lp="885,382.5",
		pos="e,838.71,189.45 875.57,575.69 871.47,567.22 866,553.56 866,541 866,541 866,541 866,224 866,211.09 856.21,200.94 845.66,193.75"];
	index_filtered_bam	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 973 440.5 973 459.5 1083 459.5 1083 440.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1028 447.5 0 94 18 -index_filtered_bam ",
		height=0.27778,
		label=index_filtered_bam,
		pos="1028,450",
		rects="973,440.5,1083,459.5",
		width=1.5278];
	extract_basename_2 -> "bowtie-se"	[_draw_="c 7 -#000000 B 10 1379.23 718.52 1367.28 715.25 1353.07 711.85 1340 710 1285.84 702.34 1148.64 704.43 1094 702 938.69 695.1 754.13 \
683.73 673.77 678.63 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 674.06 676.19 666.91 678.19 673.74 681.08 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1127.5 695.6 0 67 15 -output_filename ",
		label=output_filename,
		lp="1127.5,697.5",
		pos="e,665.4,678.09 1379.2,718.52 1367.3,715.25 1353.1,711.85 1340,710 1285.8,702.34 1148.6,704.43 1094,702 938.69,695.1 754.13,683.73 \
673.77,678.63"];
	extract_basename_2 -> remove_encode_blacklist	[_draw_="c 7 -#000000 B 10 1382.82 718.55 1365.06 710.62 1344 696.83 1344 676 1344 676 1344 676 1344 494 1344 472.45 1293.58 461.65 1246.71 \
456.27 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1247.05 453.84 1239.82 455.52 1246.52 458.71 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1389.5 583.1 0 91 20 -output_basename_file ",
		label=output_basename_file,
		lp="1389.5,585",
		pos="e,1238.3,455.35 1382.8,718.55 1365.1,710.62 1344,696.83 1344,676 1344,676 1344,676 1344,494 1344,472.45 1293.6,461.65 1246.7,456.27"];
	"preseq-c-curve"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1400.5 125.5 1400.5 144.5 1489.5 144.5 1489.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1445 132.5 0 73 14 -preseq-c-curve ",
		height=0.27778,
		label="preseq-c-curve",
		pos="1445,135",
		rects="1400.5,125.5,1489.5,144.5",
		width=1.2361];
	extract_basename_2 -> "preseq-c-curve"	[_draw_="c 7 -#000000 B 10 1456.36 718.57 1496.67 710.23 1547 695.85 1547 676 1547 676 1547 676 1547 179 1547 154.9 1522.52 144.09 1497.54 \
139.34 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1498.24 136.97 1490.94 138.24 1497.44 141.8 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1592.5 425.6 0 91 20 -output_file_basename ",
		label=output_file_basename,
		lp="1592.5,427.5",
		pos="e,1489.4,138 1456.4,718.57 1496.7,710.23 1547,695.85 1547,676 1547,676 1547,676 1547,179 1547,154.9 1522.5,144.09 1497.5,139.34"];
	extract_basename_2 -> "filter-unmapped"	[_draw_="c 7 -#000000 B 13 1375.05 718.5 1363.98 715.66 1351.48 712.57 1340 710 1301.34 701.35 1165 715.62 1165 676 1165 676 1165 676 1165 \
584 1165 567.26 1125.65 555.92 1090.25 549.11 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1091.12 546.78 1083.79 547.92 1090.23 551.6 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1198.5 628.1 0 67 15 -output_filename ",
		label=output_filename,
		lp="1198.5,630",
		pos="e,1082.3,547.64 1375.1,718.5 1364,715.66 1351.5,712.57 1340,710 1301.3,701.35 1165,715.62 1165,676 1165,676 1165,676 1165,584 1165,\
567.26 1125.6,555.92 1090.2,549.11"];
	extract_basename_2 -> execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 B 10 1418 718.52 1428.58 709.32 1443 693.56 1443 676 1443 676 1443 676 1443 494 1443 478.84 1431.17 468.92 1417.04 \
462.48 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1418.3 460.34 1410.89 459.98 1416.46 464.88 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1491.5 583.1 0 97 22 -input_output_filenames ",
		label=input_output_filenames,
		lp="1491.5,585",
		pos="e,1409.5,459.41 1418,718.52 1428.6,709.32 1443,693.56 1443,676 1443,676 1443,676 1443,494 1443,478.84 1431.2,468.92 1417,462.48"];
	mapped_filtered_reads_count -> output_read_count_mapped_filtered	[_draw_="c 7 -#000000 B 4 616.32 80.71 610.22 74.88 601.91 66.93 594.77 60.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 596.5 58.38 589.74 55.31 593.11 61.92 ",
		pos="e,588.65,54.265 616.32,80.709 610.22,74.879 601.91,66.934 594.77,60.117"];
	"preseq-c-curve" -> output_preseq_c_curve_files	[_draw_="c 7 -#000000 B 10 1489.35 130.18 1498.7 127.59 1507.87 123.47 1515 117 1531.03 102.45 1517.6 88 1531 71 1534.77 66.22 1539.71 62.09 \
1544.81 58.63 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1545.8 60.9 1550.47 55.14 1543.23 56.73 ",
		pos="e,1551.8,54.341 1489.4,130.18 1498.7,127.59 1507.9,123.47 1515,117 1531,102.45 1517.6,87.997 1531,71 1534.8,66.224 1539.7,62.088 \
1544.8,58.631"];
	percent_uniq_reads	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1359 80.5 1359 99.5 1471 99.5 1471 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1415 87.5 0 96 18 -percent_uniq_reads ",
		height=0.27778,
		label=percent_uniq_reads,
		pos="1415,90",
		rects="1359,80.5,1471,99.5",
		width=1.5556];
	"preseq-c-curve" -> percent_uniq_reads	[_draw_="c 7 -#000000 B 7 1432.36 125.66 1429.3 123.16 1426.26 120.23 1424 117 1421.96 114.09 1420.35 110.68 1419.08 107.3 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1421.46 106.7 1417.06 100.72 1416.78 108.13 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1471 110.6 0 94 22 -preseq_c_curve_outfile ",
		label=preseq_c_curve_outfile,
		lp="1471,112.5",
		pos="e,1416.6,99.277 1432.4,125.66 1429.3,123.16 1426.3,120.23 1424,117 1422,114.09 1420.3,110.68 1419.1,107.3"];
	"filter-unmapped" -> filtered2sorted	[_draw_="c 7 -#000000 B 4 1034.04 530.71 1033.44 525.59 1032.66 518.85 1031.94 512.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1034.38 512.44 1031.14 505.77 1029.51 513 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1051 515.6 0 38 10 -input_file ",
		label=input_file,
		lp="1051,517.5",
		pos="e,1031,504.27 1034,530.71 1033.4,525.59 1032.7,518.85 1031.9,512.67"];
	mark_duplicates -> output_picard_mark_duplicates_files	[_draw_="c 7 -#000000 B 10 1155.96 308.44 1177.5 302.99 1198 292.23 1198 271 1198 271 1198 271 1198 89 1198 78.86 1202.91 68.7 1208.09 60.8 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1209.82 62.6 1211.91 55.48 1205.84 59.74 ",
		pos="e,1212.8,54.255 1156,308.44 1177.5,302.99 1198,292.23 1198,271 1198,271 1198,271 1198,89 1198,78.856 1202.9,68.697 1208.1,60.803"];
	mark_duplicates -> sort_dups_marked_bams	[_draw_="c 7 -#000000 B 4 1080.53 305.5 1059.6 298.79 1030.24 289.37 1007.48 282.06 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1008.27 279.75 1000.86 279.94 1006.78 284.41 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1071 290.6 0 38 10 -input_file ",
		label=input_file,
		lp="1071,292.5",
		pos="e,999.42,279.48 1080.5,305.5 1059.6,298.79 1030.2,289.37 1007.5,282.06"];
	index_masked_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 962.5 350.5 962.5 369.5 1081.5 369.5 1081.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1022 357.5 0 103 17 -index_masked_bams ",
		height=0.27778,
		label=index_masked_bams,
		pos="1022,360",
		rects="962.5,350.5,1081.5,369.5",
		width=1.6528];
	sort_masked_bams -> index_masked_bams	[_draw_="c 7 -#000000 B 4 1022 395.71 1022 390.59 1022 383.85 1022 377.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1024.45 377.78 1022 370.78 1019.55 377.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1041 380.6 0 38 10 -input_file ",
		label=input_file,
		lp="1041,382.5",
		pos="e,1022,369.27 1022,395.71 1022,390.59 1022,383.85 1022,377.67"];
	index_bams -> bam_idxstats	[_draw_="c 7 -#000000 B 4 782.24 172.09 742.14 164.75 678.58 153.12 634.49 145.06 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 635.04 142.67 627.71 143.82 634.16 147.49 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 732.5 155.6 0 19 3 -bam ",
		label=bam,
		lp="732.5,157.5",
		pos="e,626.22,143.54 782.24,172.09 742.14,164.75 678.58,153.12 634.49,145.06"];
	percent_uniq_reads -> output_percentage_uniq_reads	[_draw_="c 7 -#000000 B 4 1413.07 80.71 1411.85 75.47 1410.24 68.53 1408.78 62.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1411.24 62 1407.27 55.74 1406.46 63.11 ",
		pos="e,1406.9,54.265 1413.1,80.709 1411.9,75.474 1410.2,68.534 1408.8,62.235"];
	index_masked_bams -> mark_duplicates	[_draw_="c 7 -#000000 B 7 1028.12 350.6 1032.71 344.86 1039.48 337.51 1047 333 1050.56 330.86 1054.41 328.98 1058.37 327.33 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1058.98 329.72 1064.67 324.97 1057.25 325.13 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1066 335.6 0 38 10 -input_file ",
		label=input_file,
		lp="1066,337.5",
		pos="e,1066.1,324.43 1028.1,350.6 1032.7,344.86 1039.5,337.51 1047,333 1050.6,330.86 1054.4,328.98 1058.4,327.33"];
	filtered2sorted -> remove_encode_blacklist	[_draw_="c 7 -#000000 B 4 1057.26 485.5 1078.91 478.76 1109.32 469.28 1132.8 461.97 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1133.39 464.35 1139.35 459.93 1131.94 459.67 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1114 470.6 0 6 1 -a ",
		label=a,
		lp="1114,472.5",
		pos="e,1140.8,459.48 1057.3,485.5 1078.9,478.76 1109.3,469.28 1132.8,461.97"];
	filtered2sorted -> index_filtered_bam	[_draw_="c 7 -#000000 B 4 1029.61 485.71 1029.38 480.59 1029.06 473.85 1028.78 467.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1031.23 467.66 1028.45 460.78 1026.33 467.88 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1048 470.6 0 38 10 -input_file ",
		label=input_file,
		lp="1048,472.5",
		pos="e,1028.4,459.27 1029.6,485.71 1029.4,480.59 1029.1,473.85 1028.8,467.67"];
	filtered2sorted -> "preseq-c-curve"	[_draw_="c 7 -#000000 B 16 1009.96 485.64 987.68 475.23 956.81 456.77 973 440 981.92 430.76 1191.83 436.11 1204 432 1228.24 423.82 1235 409.08 \
1235 383.5 1235 383.5 1235 383.5 1235 179 1235 146.9 1330.35 138.54 1392.56 136.5 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1392.28 138.95 1399.21 136.3 1392.14 134.06 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1269 313.1 0 68 17 -input_sorted_file ",
		label=input_sorted_file,
		lp="1269,315",
		pos="e,1400.7,136.26 1010,485.64 987.68,475.23 956.81,456.77 973,440 981.92,430.76 1191.8,436.11 1204,432 1228.2,423.82 1235,409.08 1235,\
383.5 1235,383.5 1235,383.5 1235,179 1235,146.9 1330.4,138.54 1392.6,136.5"];
	filtered2sorted -> execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 B 4 1073.75 488.47 1129.59 481.4 1227.07 469.08 1294.89 460.5 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1294.87 462.97 1301.51 459.66 1294.26 458.11 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1262 470.6 0 64 15 -input_bam_files ",
		label=input_bam_files,
		lp="1262,472.5",
		pos="e,1303,459.47 1073.8,488.47 1129.6,481.4 1227.1,469.08 1294.9,460.5"];
	execute_pcr_bottleneck_coef -> output_pbc_files	[_draw_="c 7 -#000000 B 13 1448.63 442.26 1491.13 436.36 1535 425.54 1535 406 1535 406 1535 406 1535 89 1535 63.23 1623.17 69.9 1648 63 1654.37 \
61.23 1661.12 59.17 1667.57 57.1 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1668.2 59.47 1674.1 54.97 1666.68 54.81 ",
		pos="e,1675.5,54.498 1448.6,442.26 1491.1,436.36 1535,425.54 1535,406 1535,406 1535,406 1535,89 1535,63.233 1623.2,69.899 1648,63 1654.4,\
61.23 1661.1,59.165 1667.6,57.098"];
	index_dups_marked_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 900 215.5 900 234.5 1046 234.5 1046 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 973 222.5 0 130 22 -index_dups_marked_bams ",
		height=0.27778,
		label=index_dups_marked_bams,
		pos="973,225",
		rects="900,215.5,1046,234.5",
		width=2.0278];
	index_dups_marked_bams -> output_data_sorted_dups_marked_bam_files	[_draw_="c 7 -#000000 B 10 982.14 215.74 989.97 207.71 1000 194.75 1000 181 1000 181 1000 181 1000 89 1000 80.31 1000.21 70.62 1000.43 62.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1002.88 62.83 1000.65 55.75 997.98 62.68 ",
		pos="e,1000.7,54.242 982.14,215.74 989.97,207.71 1000,194.75 1000,181 1000,181 1000,181 1000,89 1000,80.305 1000.2,70.624 1000.4,62.653"];
	index_dups_marked_bams -> remove_duplicates	[_draw_="c 7 -#000000 B 4 962.13 215.5 954.53 209.56 944.2 201.48 935.44 194.64 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 937.06 192.79 930.04 190.41 934.04 196.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 969 200.6 0 38 10 -input_file ",
		label=input_file,
		lp="969,202.5",
		pos="e,928.84,189.48 962.13,215.5 954.53,209.56 944.2,201.48 935.44,194.64"];
	sort_dups_marked_bams -> index_dups_marked_bams	[_draw_="c 7 -#000000 B 4 973 260.71 973 255.59 973 248.85 973 242.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 975.45 242.78 973 235.78 970.55 242.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 992 245.6 0 38 10 -input_file ",
		label=input_file,
		lp="992,247.5",
		pos="e,973,234.27 973,260.71 973,255.59 973,248.85 973,242.67"];
	masked_file_basename -> mark_duplicates	[_draw_="c 7 -#000000 B 4 1156.73 395.56 1147.5 380.81 1128.32 350.11 1116.66 331.46 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1118.77 330.2 1112.98 325.57 1114.61 332.8 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1172.5 358.1 0 67 15 -output_filename ",
		label=output_filename,
		lp="1172.5,360",
		pos="e,1112.2,324.28 1156.7,395.56 1147.5,380.81 1128.3,350.11 1116.7,331.46"];
}