digraph workflow {
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		output_picard_mark_duplicates_files	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1121.5 35.5 1121.5 54.5 1316.5 54.5 1316.5 35.5 ",
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	}
	mark_duplicates	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1076 305.5 1076 324.5 1174 324.5 1174 305.5 ",
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	picard_java_opts -> mark_duplicates	[_draw_="c 7 -#000000 B 16 1017.42 718.53 1026.41 715.67 1036.61 712.55 1046 710 1092.53 697.38 1149 724.21 1149 676 1149 676 1149 676 1149 \
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		rects="1156.5,440.5,1297.5,459.5",
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	ENCODE_blacklist_bedfile -> remove_encode_blacklist	[_draw_="c 7 -#000000 B 10 1134.76 718.55 1141.49 714.47 1148.59 708.93 1153 702 1172.84 670.8 1157.67 655.78 1167 620 1182.02 562.42 1208.06 \
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	picard_jar_path -> mark_duplicates	[_draw_="c 7 -#000000 B 22 912.58 718.63 921.48 715.37 932.11 711.95 942 710 955.98 707.24 1058.97 711.02 1070 702 1079.27 694.43 1077 687.97 \
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	nthreads -> "bowtie-se"	[_draw_="c 7 -#000000 B 13 798.35 718.53 792.58 715.33 785.67 712 779 710 746.89 700.38 735.19 714.27 704 702 697.8 699.56 698 695.91 692 \
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		width=1.5417];
	nthreads -> sort_masked_bams	[_draw_="c 7 -#000000 B 13 828.46 718.61 848.59 707.79 880 688.84 880 676 880 676 880 676 880 471.5 880 457.16 876.63 449.9 887 440 905.56 \
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	nthreads -> sort_dedup_bams	[_draw_="c 7 -#000000 B 13 795.57 718.53 788.35 714.26 780.15 708.58 774 702 742.9 668.71 732 654.06 732 608.5 732 608.5 732 608.5 732 426.5 \
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 750.5 425.6 0 37 8 -nthreads ",
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		pos="e,767.22,144.04 795.57,718.53 788.35,714.26 780.15,708.58 774,702 742.9,668.71 732,654.06 732,608.5 732,608.5 732,608.5 732,426.5 \
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		height=0.27778,
		label=sort_bams,
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	nthreads -> sort_bams	[_draw_="c 7 -#000000 B 7 813.56 718.7 814.41 713.85 815.41 707.6 816 702 819.7 666.9 821.15 625.58 821.69 602.95 ",
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	nthreads -> filtered2sorted	[_draw_="c 7 -#000000 B 13 826.87 718.53 832.69 715.49 839.52 712.26 846 710 882.09 697.41 925 714.22 925 676 925 676 925 676 925 539 925 \
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 943.5 605.6 0 37 8 -nthreads ",
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	sam2bam	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 739.5 620.5 739.5 639.5 804.5 639.5 804.5 620.5 ",
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		height=0.27778,
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	nthreads -> sam2bam	[_draw_="c 7 -#000000 B 7 799.7 718.64 789.85 711.14 776.76 699.16 771 685 766.19 673.19 766.77 658.7 768.37 647.7 ",
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		rects="864,260.5,1002,279.5",
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	nthreads -> sort_dups_marked_bams	[_draw_="c 7 -#000000 B 22 812.63 718.59 814.3 693.82 817.93 621.72 805 603 800.02 595.8 792.21 602.04 787 595 763.03 562.61 778.45 545.22 \
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855.76 278.89 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 856.07 281.32 862.63 277.86 855.34 276.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 794.5 493.1 0 37 8 -nthreads ",
		label=nthreads,
		lp="794.5,495",
		pos="e,864.12,277.63 812.63,718.59 814.3,693.82 817.93,621.72 805,603 800.02,595.8 792.21,602.04 787,595 763.03,562.61 778.45,545.22 \
776,505 775.46,496.13 775.61,493.88 776,485 776.22,479.87 777,478.63 777,473.5 777,473.5 777,473.5 777,314 777,295.9 816.51,285.13 \
855.76,278.89"];
	genome_ref_first_index_file -> "bowtie-se"	[_draw_="c 7 -#000000 B 7 530.35 718.53 512.51 713.52 501.13 705.58 512 693 521.66 681.82 557.67 677.85 587.03 676.51 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 587.09 678.96 593.99 676.25 586.9 674.07 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 567.5 695.6 0 111 27 -genome_ref_first_index_file ",
		label=genome_ref_first_index_file,
		lp="567.5,697.5",
		pos="e,595.5,676.19 530.35,718.53 512.51,713.52 501.13,705.58 512,693 521.66,681.82 557.67,677.85 587.03,676.51"];
	execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 1317 440.5 1317 459.5 1475 459.5 1475 440.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1396 447.5 0 142 27 -execute_pcr_bottleneck_coef ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label=execute_pcr_bottleneck_coef,
		pos="1396,450",
		rects="1317,440.5,1475,459.5",
		width=2.1944];
	genome_sizes_file -> execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 B 13 1245.74 718.7 1245.44 708.6 1245 691.05 1245 676 1245 676 1245 676 1245 606.5 1245 592.47 1240.65 587.51 1247 \
575 1274.28 521.3 1336.24 482.08 1371.05 463.34 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1372.07 465.58 1377.12 460.15 1369.79 461.24 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1276.5 583.1 0 59 12 -genome_sizes ",
		label=genome_sizes,
		lp="1276.5,585",
		pos="e,1378.5,459.44 1245.7,718.7 1245.4,708.6 1245,691.05 1245,676 1245,676 1245,676 1245,606.5 1245,592.47 1240.6,587.51 1247,575 1274.3,\
521.3 1336.2,482.08 1371.1,463.34"];
	extract_basename_1	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 992.5 790.5 992.5 809.5 1111.5 809.5 1111.5 790.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1052 797.5 0 103 18 -extract_basename_1 ",
		height=0.27778,
		label=extract_basename_1,
		pos="1052,800",
		rects="992.5,790.5,1111.5,809.5",
		width=1.6528];
	input_fastq_files -> extract_basename_1	[_draw_="c 7 -#000000 B 7 739.37 737.42 749.4 745.91 766.14 758.63 783 765 848.45 789.72 928.57 797.2 984.26 799.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 984.06 801.57 991.13 799.33 984.21 796.67 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 858 775.6 0 38 10 -input_file ",
		label=input_file,
		lp="858,777.5",
		pos="e,992.64,799.38 739.37,737.42 749.4,745.91 766.14,758.63 783,765 848.45,789.72 928.57,797.2 984.26,799.12"];
	input_fastq_files -> "bowtie-se"	[_draw_="c 7 -#000000 B 10 706.65 718.57 697.76 715.58 687.49 712.36 678 710 657.86 704.99 646.53 716.82 632 702 629.55 699.5 628.21 696.17 \
627.53 692.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 629.99 692.69 627.06 685.88 625.1 693.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 663.5 695.6 0 63 16 -input_fastq_file ",
		label=input_fastq_file,
		lp="663.5,697.5",
		pos="e,626.96,684.37 706.65,718.57 697.76,715.58 687.49,712.36 678,710 657.86,704.99 646.53,716.82 632,702 629.55,699.5 628.21,696.17 \
627.53,692.73"];
	extract_basename_2	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1316.5 718.5 1316.5 737.5 1435.5 737.5 1435.5 718.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1376 725.5 0 103 18 -extract_basename_2 ",
		height=0.27778,
		label=extract_basename_2,
		pos="1376,728",
		rects="1316.5,718.5,1435.5,737.5",
		width=1.6528];
	extract_basename_2 -> remove_encode_blacklist	[_draw_="c 7 -#000000 B 10 1351.44 718.66 1333.39 710.79 1312 697.03 1312 676 1312 676 1312 676 1312 606.5 1312 548.07 1265.22 490.76 1241.07 \
465.06 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1243.13 463.66 1236.51 460.32 1239.6 467.06 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1356.5 583.1 0 91 20 -output_basename_file ",
		label=output_basename_file,
		lp="1356.5,585",
		pos="e,1235.5,459.23 1351.4,718.66 1333.4,710.79 1312,697.03 1312,676 1312,676 1312,676 1312,606.5 1312,548.07 1265.2,490.76 1241.1,465.06"];
	extract_basename_2 -> execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 B 10 1386.31 718.8 1396.64 709.59 1411 693.61 1411 676 1411 676 1411 676 1411 494 1411 484.61 1407.77 474.68 1404.31 \
466.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1406.63 465.89 1401.4 460.63 1402.21 468.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1459.5 583.1 0 97 22 -input_output_filenames ",
		label=input_output_filenames,
		lp="1459.5,585",
		pos="e,1400.7,459.27 1386.3,718.8 1396.6,709.59 1411,693.61 1411,676 1411,676 1411,676 1411,494 1411,484.61 1407.8,474.68 1404.3,466.73"];
	extract_basename_2 -> "bowtie-se"	[_draw_="c 7 -#000000 B 10 1347.9 718.52 1336.01 715.28 1321.94 711.92 1309 710 1278.96 705.55 793.32 686.7 763 685 731.36 683.22 695.58 \
680.82 668.81 678.94 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 669.11 676.51 661.96 678.46 668.77 681.4 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1189.5 695.6 0 67 15 -output_filename ",
		label=output_filename,
		lp="1189.5,697.5",
		pos="e,660.45,678.35 1347.9,718.52 1336,715.28 1321.9,711.92 1309,710 1279,705.55 793.32,686.7 763,685 731.36,683.22 695.58,680.82 668.81,\
678.94"];
	"filter-unmapped"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 932.5 530.5 932.5 549.5 1027.5 549.5 1027.5 530.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 980 537.5 0 79 15 -filter-unmapped ",
		height=0.27778,
		label="filter-unmapped",
		pos="980,540",
		rects="932.5,530.5,1027.5,549.5",
		width=1.3194];
	extract_basename_2 -> "filter-unmapped"	[_draw_="c 7 -#000000 B 7 1351.21 718.58 1338.21 714 1322.11 708.04 1308 702 1190.99 651.93 1055.92 581.45 1002.97 553.31 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1004.43 551.31 997.1 550.18 1002.13 555.64 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1204.5 628.1 0 67 15 -output_filename ",
		label=output_filename,
		lp="1204.5,630",
		pos="e,995.77,549.47 1351.2,718.58 1338.2,714 1322.1,708.04 1308,702 1191,651.93 1055.9,581.45 1003,553.31"];
	"preseq-c-curve"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1396.5 125.5 1396.5 144.5 1485.5 144.5 1485.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1441 132.5 0 73 14 -preseq-c-curve ",
		height=0.27778,
		label="preseq-c-curve",
		pos="1441,135",
		rects="1396.5,125.5,1485.5,144.5",
		width=1.2361];
	extract_basename_2 -> "preseq-c-curve"	[_draw_="c 7 -#000000 B 10 1425.01 718.51 1465.03 710.13 1515 695.73 1515 676 1515 676 1515 676 1515 179 1515 163.82 1503.21 153.9 1489.04 \
147.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1490.28 145.33 1482.87 144.98 1488.44 149.87 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1560.5 425.6 0 91 20 -output_file_basename ",
		label=output_file_basename,
		lp="1560.5,427.5",
		pos="e,1481.5,144.42 1425,718.51 1465,710.13 1515,695.73 1515,676 1515,676 1515,676 1515,179 1515,163.82 1503.2,153.9 1489,147.47"];
	index_dups_marked_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 860 215.5 860 234.5 1006 234.5 1006 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 933 222.5 0 130 22 -index_dups_marked_bams ",
		height=0.27778,
		label=index_dups_marked_bams,
		pos="933,225",
		rects="860,215.5,1006,234.5",
		width=2.0278];
	index_dups_marked_bams -> output_data_sorted_dups_marked_bam_files	[_draw_="c 7 -#000000 B 13 944.95 215.52 947.87 213.03 950.79 210.12 953 207 960.16 196.9 963 193.38 963 181 963 181 963 181 963 89 963 77.23 \
971.07 67.07 979.67 59.59 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 981.06 61.61 985.04 55.35 978.02 57.77 ",
		pos="e,986.22,54.413 944.95,215.52 947.87,213.03 950.79,210.12 953,207 960.16,196.9 963,193.38 963,181 963,181 963,181 963,89 963,77.228 \
971.07,67.075 979.67,59.595"];
	remove_duplicates	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 833 170.5 833 189.5 943 189.5 943 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 888 177.5 0 94 17 -remove_duplicates ",
		height=0.27778,
		label=remove_duplicates,
		pos="888,180",
		rects="833,170.5,943,189.5",
		width=1.5278];
	index_dups_marked_bams -> remove_duplicates	[_draw_="c 7 -#000000 B 4 924.32 215.71 918.22 209.88 909.91 201.93 902.77 195.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 904.5 193.38 897.74 190.31 901.11 196.92 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 933 200.6 0 38 10 -input_file ",
		label=input_file,
		lp="933,202.5",
		pos="e,896.65,189.27 924.32,215.71 918.22,209.88 909.91,201.93 902.77,195.12"];
	percent_uniq_reads	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1353 80.5 1353 99.5 1465 99.5 1465 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1409 87.5 0 96 18 -percent_uniq_reads ",
		height=0.27778,
		label=percent_uniq_reads,
		pos="1409,90",
		rects="1353,80.5,1465,99.5",
		width=1.5556];
	percent_uniq_reads -> output_percentage_uniq_reads	[_draw_="c 7 -#000000 B 4 1408.04 80.71 1407.44 75.59 1406.66 68.85 1405.94 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1408.38 62.44 1405.14 55.77 1403.51 63 ",
		pos="e,1405,54.265 1408,80.709 1407.4,75.593 1406.7,68.848 1405.9,62.666"];
	mark_duplicates -> output_picard_mark_duplicates_files	[_draw_="c 7 -#000000 B 10 1094.24 305.51 1078.25 299.03 1062 288.22 1062 271 1062 271 1062 271 1062 89 1062 78.19 1118.06 64.95 1163.19 \
56.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1163.58 58.45 1169.98 54.71 1162.64 53.65 ",
		pos="e,1171.5,54.424 1094.2,305.51 1078.2,299.03 1062,288.22 1062,271 1062,271 1062,271 1062,89 1062,78.192 1118.1,64.946 1163.2,56.035"];
	mark_duplicates -> sort_dups_marked_bams	[_draw_="c 7 -#000000 B 10 1076.2 305.68 1074.78 305.45 1073.38 305.22 1072 305 1048.92 301.26 1042.81 302.14 1020 297 1001.93 292.93 982.11 \
287.12 965.97 282.02 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 966.74 279.7 959.33 279.89 965.25 284.36 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1039 290.6 0 38 10 -input_file ",
		label=input_file,
		lp="1039,292.5",
		pos="e,957.89,279.43 1076.2,305.68 1074.8,305.45 1073.4,305.22 1072,305 1048.9,301.26 1042.8,302.14 1020,297 1001.9,292.93 982.11,287.12 \
965.97,282.02"];
	index_dedup_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 719.5 80.5 719.5 99.5 830.5 99.5 830.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 775 87.5 0 95 16 -index_dedup_bams ",
		height=0.27778,
		label=index_dedup_bams,
		pos="775,90",
		rects="719.5,80.5,830.5,99.5",
		width=1.5417];
	index_dedup_bams -> output_data_sorted_dedup_bam_files	[_draw_="c 7 -#000000 B 4 775.77 80.71 776.25 75.59 776.87 68.85 777.45 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 779.88 62.97 778.09 55.77 775 62.52 ",
		pos="e,778.23,54.265 775.77,80.709 776.25,75.593 776.87,68.848 777.45,62.666"];
	masked_file_basename	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1158.5 395.5 1158.5 414.5 1289.5 414.5 1289.5 395.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1224 402.5 0 115 20 -masked_file_basename ",
		height=0.27778,
		label=masked_file_basename,
		pos="1224,405",
		rects="1158.5,395.5,1289.5,414.5",
		width=1.8194];
	remove_encode_blacklist -> masked_file_basename	[_draw_="c 7 -#000000 B 4 1226.42 440.71 1226.06 435.59 1225.59 428.85 1225.16 422.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1227.61 422.59 1224.68 415.78 1222.73 422.93 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1244 425.6 0 38 10 -input_file ",
		label=input_file,
		lp="1244,427.5",
		pos="e,1224.6,414.27 1226.4,440.71 1226.1,435.59 1225.6,428.85 1225.2,422.67"];
	remove_encode_blacklist -> sort_masked_bams	[_draw_="c 7 -#000000 B 4 1198.35 440.5 1175.51 433.73 1143.38 424.2 1118.66 416.87 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1119.45 414.55 1112.04 414.91 1118.05 419.25 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1186 425.6 0 38 10 -input_file ",
		label=input_file,
		lp="1186,427.5",
		pos="e,1110.6,414.48 1198.4,440.5 1175.5,433.73 1143.4,424.2 1118.7,416.87"];
	bam_idxstats	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 443.5 125.5 443.5 144.5 526.5 144.5 526.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 485 132.5 0 67 12 -bam_idxstats ",
		height=0.27778,
		label=bam_idxstats,
		pos="485,135",
		rects="443.5,125.5,526.5,144.5",
		width=1.1528];
	percent_mitochondrial_reads	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 350 80.5 350 99.5 508 99.5 508 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 429 87.5 0 142 27 -percent_mitochondrial_reads ",
		height=0.27778,
		label=percent_mitochondrial_reads,
		pos="429,90",
		rects="350,80.5,508,99.5",
		width=2.1944];
	bam_idxstats -> percent_mitochondrial_reads	[_draw_="c 7 -#000000 B 4 473.94 125.5 466.19 119.56 455.67 111.48 446.76 104.64 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 448.29 102.72 441.24 100.4 445.3 106.61 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 478.5 110.6 0 33 8 -idxstats ",
		label=idxstats,
		lp="478.5,112.5",
		pos="e,440.04,99.478 473.94,125.5 466.19,119.56 455.67,111.48 446.76,104.64"];
	index_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 609 170.5 609 189.5 685 189.5 685 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 647 177.5 0 60 10 -index_bams ",
		height=0.27778,
		label=index_bams,
		pos="647,180",
		rects="609,170.5,685,189.5",
		width=1.0556];
	index_bams -> bam_idxstats	[_draw_="c 7 -#000000 B 4 614.99 170.5 589.14 163.64 552.63 153.95 524.88 146.59 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 525.8 144.29 518.4 144.87 524.54 149.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 589.5 155.6 0 19 3 -bam ",
		label=bam,
		lp="589.5,157.5",
		pos="e,516.94,144.48 614.99,170.5 589.14,163.64 552.63,153.95 524.88,146.59"];
	execute_pcr_bottleneck_coef -> output_pbc_files	[_draw_="c 7 -#000000 B 13 1403.36 440.92 1430.86 409.87 1526 294.25 1526 181 1526 181 1526 181 1526 89 1526 61.5 1620.45 70.17 1647 63 1653.45 \
61.26 1660.28 59.19 1666.79 57.11 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1667.49 59.46 1673.38 54.96 1665.97 54.8 ",
		pos="e,1674.8,54.485 1403.4,440.92 1430.9,409.87 1526,294.25 1526,181 1526,181 1526,181 1526,89 1526,61.497 1620.4,70.172 1647,63 1653.4,\
61.259 1660.3,59.191 1666.8,57.109"];
	extract_basename_1 -> extract_basename_2	[_draw_="c 7 -#000000 B 7 1111.25 797.21 1164.21 794.2 1243.36 786.19 1309 765 1326.02 759.51 1343.78 749.75 1356.74 741.78 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1357.88 743.96 1362.49 738.15 1355.26 739.81 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1293 775.6 0 36 9 -file_path ",
		label=file_path,
		lp="1293,777.5",
		pos="e,1363.8,737.34 1111.2,797.21 1164.2,794.2 1243.4,786.19 1309,765 1326,759.51 1343.8,749.75 1356.7,741.78"];
	masked_file_basename -> mark_duplicates	[_draw_="c 7 -#000000 B 7 1217.09 395.92 1204.99 382.04 1178.78 353.24 1153 333 1151.15 331.55 1149.18 330.13 1147.16 328.76 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1148.76 326.88 1141.54 325.18 1146.12 331.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1226.5 358.1 0 67 15 -output_filename ",
		label=output_filename,
		lp="1226.5,360",
		pos="e,1140.3,324.36 1217.1,395.92 1205,382.04 1178.8,353.24 1153,333 1151.2,331.55 1149.2,330.13 1147.2,328.76"];
	"bowtie-se" -> output_bowtie_log	[_draw_="c 7 -#000000 B 10 595.52 673.29 510.15 670.99 286 662.01 286 631 286 631 286 631 286 89 286 74.75 274.68 64.77 261.88 58.03 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 262.99 55.85 255.61 55.08 260.9 60.28 ",
		pos="e,254.24,54.437 595.52,673.29 510.15,670.99 286,662.01 286,631 286,631 286,631 286,89 286,74.752 274.68,64.769 261.88,58.034"];
	mapped_reads_count	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 43.5 80.5 43.5 99.5 164.5 99.5 164.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 104 87.5 0 105 18 -mapped_reads_count ",
		height=0.27778,
		label=mapped_reads_count,
		pos="104,90",
		rects="43.5,80.5,164.5,99.5",
		width=1.6806];
	"bowtie-se" -> mapped_reads_count	[_draw_="c 7 -#000000 B 10 595.72 674.36 491.25 675.1 169 673.92 169 631 169 631 169 631 169 134 169 119.27 157.25 109.3 143.74 102.69 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 144.9 100.52 137.51 99.97 142.94 105.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 191.5 380.6 0 45 10 -bowtie_log ",
		label=bowtie_log,
		lp="191.5,382.5",
		pos="e,136.12,99.361 595.72,674.36 491.25,675.1 169,673.92 169,631 169,631 169,631 169,134 169,119.27 157.25,109.3 143.74,102.69"];
	"bowtie-se" -> sam2bam	[_draw_="c 7 -#000000 B 4 656.45 665.5 679.13 658.73 711.05 649.2 735.59 641.87 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 736.15 644.26 742.16 639.91 734.75 639.57 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 731 650.6 0 38 10 -input_file ",
		label=input_file,
		lp="731,652.5",
		pos="e,743.61,639.48 656.45,665.5 679.13,658.73 711.05,649.2 735.59,641.87"];
	index_masked_bams	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1022.5 350.5 1022.5 369.5 1141.5 369.5 1141.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1082 357.5 0 103 17 -index_masked_bams ",
		height=0.27778,
		label=index_masked_bams,
		pos="1082,360",
		rects="1022.5,350.5,1141.5,369.5",
		width=1.6528];
	sort_masked_bams -> index_masked_bams	[_draw_="c 7 -#000000 B 4 1082 395.71 1082 390.59 1082 383.85 1082 377.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1084.45 377.78 1082 370.78 1079.55 377.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1101 380.6 0 38 10 -input_file ",
		label=input_file,
		lp="1101,382.5",
		pos="e,1082,369.27 1082,395.71 1082,390.59 1082,383.85 1082,377.67"];
	sort_dedup_bams -> index_dedup_bams	[_draw_="c 7 -#000000 B 4 770.16 125.71 770.87 120.59 771.81 113.85 772.67 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 775.1 108.04 773.64 100.76 770.24 107.36 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 791 110.6 0 38 10 -input_file ",
		label=input_file,
		lp="791,112.5",
		pos="e,773.85,99.265 770.16,125.71 770.87,120.59 771.81,113.85 772.67,107.67"];
	mapped_filtered_reads_count	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 540.5 80.5 540.5 99.5 701.5 99.5 701.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 621 87.5 0 145 27 -mapped_filtered_reads_count ",
		height=0.27778,
		label=mapped_filtered_reads_count,
		pos="621,90",
		rects="540.5,80.5,701.5,99.5",
		width=2.2361];
	sort_dedup_bams -> mapped_filtered_reads_count	[_draw_="c 7 -#000000 B 7 739.58 125.55 730.13 122.83 719.62 119.79 710 117 692.89 112.03 673.93 106.5 657.93 101.82 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 658.71 99.5 651.3 99.88 657.33 104.2 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 740 110.6 0 60 14 -input_bam_file ",
		label=input_bam_file,
		lp="740,112.5",
		pos="e,649.85,99.458 739.58,125.55 730.13,122.83 719.62,119.79 710,117 692.89,112.03 673.93,106.5 657.93,101.82"];
	sort_bams -> index_bams	[_draw_="c 7 -#000000 B 10 822 575.69 821.87 558.55 820.78 518.11 814 485 795.48 394.54 795.47 367.2 748 288 724.91 249.48 685.9 213.4 663.73 \
194.58 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 665.52 192.89 658.58 190.28 662.38 196.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 812 380.6 0 38 10 -input_file ",
		label=input_file,
		lp="812,382.5",
		pos="e,657.42,189.31 822,575.69 821.87,558.55 820.78,518.11 814,485 795.48,394.54 795.47,367.2 748,288 724.91,249.48 685.9,213.4 663.73,\
194.58"];
	sort_bams -> "filter-unmapped"	[_draw_="c 7 -#000000 B 7 824.6 575.55 826.88 569.63 830.82 562.07 837 558 851.14 548.67 890.38 544.46 924.19 542.56 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 924.27 545 931.14 542.2 924.02 540.11 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 856 560.6 0 38 10 -input_file ",
		label=input_file,
		lp="856,562.5",
		pos="e,932.65,542.12 824.6,575.55 826.88,569.63 830.82,562.07 837,558 851.14,548.67 890.38,544.46 924.19,542.56"];
	filtered2sorted -> remove_encode_blacklist	[_draw_="c 7 -#000000 B 7 980.76 485.7 983.23 479.69 987.48 471.96 994 468 1007.1 460.04 1086.02 455.55 1148.43 453.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1148.31 455.67 1155.21 452.96 1148.13 450.77 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 997 470.6 0 6 1 -a ",
		label=a,
		lp="997,472.5",
		pos="e,1156.7,452.91 980.76,485.7 983.23,479.69 987.48,471.96 994,468 1007.1,460.04 1086,455.55 1148.4,453.21"];
	filtered2sorted -> execute_pcr_bottleneck_coef	[_draw_="c 7 -#000000 B 7 1021.85 489.02 1069.58 483.63 1148.18 474.91 1216 468 1225.64 467.02 1267.87 463.03 1309 459.16 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1309.22 461.6 1315.96 458.5 1308.77 456.72 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1248 470.6 0 64 15 -input_bam_files ",
		label=input_bam_files,
		lp="1248,472.5",
		pos="e,1317.5,458.36 1021.8,489.02 1069.6,483.63 1148.2,474.91 1216,468 1225.6,467.02 1267.9,463.03 1309,459.16"];
	index_filtered_bam	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 887 440.5 887 459.5 997 459.5 997 440.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 942 447.5 0 94 18 -index_filtered_bam ",
		height=0.27778,
		label=index_filtered_bam,
		pos="942,450",
		rects="887,440.5,997,459.5",
		width=1.5278];
	filtered2sorted -> index_filtered_bam	[_draw_="c 7 -#000000 B 7 945.25 485.53 941.62 483.32 938.37 480.52 936 477 934.07 474.14 933.77 470.75 934.32 467.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 936.63 468.19 936.49 460.78 931.97 466.66 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 955 470.6 0 38 10 -input_file ",
		label=input_file,
		lp="955,472.5",
		pos="e,936.96,459.34 945.25,485.53 941.62,483.32 938.37,480.52 936,477 934.07,474.14 933.77,470.75 934.32,467.38"];
	filtered2sorted -> "preseq-c-curve"	[_draw_="c 7 -#000000 B 19 978.73 485.62 979.55 480.18 981.29 473.16 985 468 988.74 462.79 993.38 465.29 997 460 1005.11 448.17 1004 442.84 \
1004 428.5 1004 428.5 1004 428.5 1004 314 1004 308.47 1010.41 288.62 1011 288 1113.62 179.71 1298.12 148.48 1388.38 139.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1388.57 141.99 1395.31 138.89 1388.11 137.11 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1038 313.1 0 68 17 -input_sorted_file ",
		label=input_sorted_file,
		lp="1038,315",
		pos="e,1396.8,138.75 978.73,485.62 979.55,480.18 981.29,473.16 985,468 988.74,462.79 993.38,465.29 997,460 1005.1,448.17 1004,442.84 \
1004,428.5 1004,428.5 1004,428.5 1004,314 1004,308.47 1010.4,288.62 1011,288 1113.6,179.71 1298.1,148.48 1388.4,139.55"];
	"filter-unmapped" -> filtered2sorted	[_draw_="c 7 -#000000 B 4 979.61 530.71 979.38 525.59 979.06 518.85 978.78 512.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 981.23 512.66 978.45 505.78 976.33 512.88 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 998 515.6 0 38 10 -input_file ",
		label=input_file,
		lp="998,517.5",
		pos="e,978.38,504.27 979.61,530.71 979.38,525.59 979.06,518.85 978.78,512.67"];
	"preseq-c-curve" -> output_preseq_c_curve_files	[_draw_="c 7 -#000000 B 10 1485.33 129.1 1493.29 126.51 1500.96 122.67 1507 117 1522.68 102.28 1508.17 87.47 1522 71 1526.26 65.92 1531.83 \
61.73 1537.63 58.32 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1538.64 60.56 1543.68 55.13 1536.35 56.23 ",
		pos="e,1545,54.419 1485.3,129.1 1493.3,126.51 1501,122.67 1507,117 1522.7,102.28 1508.2,87.467 1522,71 1526.3,65.924 1531.8,61.73 1537.6,\
58.323"];
	"preseq-c-curve" -> percent_uniq_reads	[_draw_="c 7 -#000000 B 7 1424.99 125.61 1421.62 123.22 1418.37 120.34 1416 117 1413.98 114.17 1412.55 110.79 1411.53 107.41 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1413.98 107.15 1410.07 100.85 1409.19 108.21 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1463 110.6 0 94 22 -preseq_c_curve_outfile ",
		label=preseq_c_curve_outfile,
		lp="1463,112.5",
		pos="e,1409.7,99.368 1425,125.61 1421.6,123.22 1418.4,120.34 1416,117 1414,114.17 1412.5,110.79 1411.5,107.41"];
	index_masked_bams -> mark_duplicates	[_draw_="c 7 -#000000 B 7 1089.78 350.7 1094.67 345.55 1101.13 338.82 1107 333 1108.01 332 1109.05 330.98 1110.11 329.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1111.66 331.86 1115.03 325.26 1108.28 328.32 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1126 335.6 0 38 10 -input_file ",
		label=input_file,
		lp="1126,337.5",
		pos="e,1116.1,324.22 1089.8,350.7 1094.7,345.55 1101.1,338.82 1107,333 1108,332 1109.1,330.98 1110.1,329.95"];
	mapped_reads_count -> output_read_count_mapped	[_draw_="c 7 -#000000 B 4 101.69 80.71 100.23 75.47 98.29 68.53 96.53 62.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 98.95 61.81 94.71 55.72 94.24 63.12 ",
		pos="e,94.307,54.265 101.69,80.709 100.23,75.474 98.288,68.534 96.531,62.235"];
	sam2bam -> sort_bams	[_draw_="c 7 -#000000 B 7 773.4 620.82 774.75 615.19 777.3 607.87 782 603 783.47 601.48 785.09 600.09 786.82 598.82 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 787.93 601.01 792.62 595.27 785.37 596.84 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 801 605.6 0 38 10 -input_file ",
		label=input_file,
		lp="801,607.5",
		pos="e,793.91,594.48 773.4,620.82 774.75,615.19 777.3,607.87 782,603 783.47,601.48 785.09,600.09 786.82,598.82"];
	remove_duplicates -> sort_dedup_bams	[_draw_="c 7 -#000000 B 4 864.49 170.5 846.15 163.88 820.51 154.61 800.42 147.35 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 801.3 145.07 793.89 144.99 799.64 149.68 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 858 155.6 0 38 10 -input_file ",
		label=input_file,
		lp="858,157.5",
		pos="e,792.46,144.48 864.49,170.5 846.15,163.88 820.51,154.61 800.42,147.35"];
	sort_dups_marked_bams -> index_dups_marked_bams	[_draw_="c 7 -#000000 B 4 933 260.71 933 255.59 933 248.85 933 242.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 935.45 242.78 933 235.78 930.55 242.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 952 245.6 0 38 10 -input_file ",
		label=input_file,
		lp="952,247.5",
		pos="e,933,234.27 933,260.71 933,255.59 933,248.85 933,242.67"];
	percent_mitochondrial_reads -> output_percent_mitochondrial_reads	[_draw_="c 7 -#000000 B 4 419.75 80.71 413.1 74.76 404.01 66.61 396.29 59.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 398.2 58.12 391.35 55.28 394.93 61.77 ",
		pos="e,390.23,54.265 419.75,80.709 413.1,74.76 404.01,66.609 396.29,59.701"];
	mapped_filtered_reads_count -> output_read_count_mapped_filtered	[_draw_="c 7 -#000000 B 4 612.9 80.71 607.21 74.88 599.45 66.93 592.79 60.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 594.77 58.64 588.13 55.35 591.27 62.07 ",
		pos="e,587.07,54.265 612.9,80.709 607.21,74.879 599.45,66.934 592.79,60.117"];
}