digraph workflow { graph [_draw_="c 9 -#fffffe00 C 7 -#eeeeee P 4 0 0 0 770.5 1359 770.5 1359 0 ", bb="0,0,1359,770.5", bgcolor="#eeeeee", clusterrank=local, color=black, dpi=96, fontsize=10, labeljust=left, nodesep=0.05, ranksep=0.22, xdotversion=1.7 ]; node [color=black, fillcolor=lightgoldenrodyellow, fontcolor=black, fontname=Helvetica, fontsize=10, height=0, label="\N", shape=record, style=filled, width=0 ]; edge [arrowsize=0.7, color=black, fontcolor=black, fontname=Helvetica, fontsize=8 ]; subgraph cluster_inputs { graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 76 639 76 713 1351 713 1351 639 ", _ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 126 701 0 84 15 -Workflow Inputs ", bb="76,639,1351,713", label="Workflow Inputs", lheight=0.15, lp="126,703.5", lwidth=1.17, rank=same, style=dashed ]; nthreads [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 611.5 647.5 611.5 666.5 670.5 666.5 670.5 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 641 654.5 0 43 8 -nthreads ", fillcolor="#94DDF4", height=0.27778, label=nthreads, pos="641,657", rects="611.5,647.5,670.5,666.5", width=0.81944]; picard_java_opts [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1147.5 647.5 1147.5 666.5 1246.5 666.5 1246.5 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1197 654.5 0 83 16 -picard_java_opts ", fillcolor="#94DDF4", height=0.27778, label=picard_java_opts, pos="1197,657", rects="1147.5,647.5,1246.5,666.5", width=1.375]; fgbio_jar_path [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1057 647.5 1057 666.5 1143 666.5 1143 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1100 654.5 0 70 14 -fgbio_jar_path ", fillcolor="#94DDF4", height=0.27778, label=fgbio_jar_path, pos="1100,657", rects="1057,647.5,1143,666.5", width=1.1944]; input_fastq_read2_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 196 647.5 196 666.5 326 666.5 326 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 261 654.5 0 114 23 -input_fastq_read2_files ", fillcolor="#94DDF4", height=0.27778, label=input_fastq_read2_files, pos="261,657", rects="196,647.5,326,666.5", width=1.8056]; regions_bed_file [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 809 647.5 809 666.5 905 666.5 905 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 857 654.5 0 80 16 -regions_bed_file ", fillcolor="#94DDF4", height=0.27778, label=regions_bed_file, pos="857,657", rects="809,647.5,905,666.5", width=1.3333]; input_fastq_read1_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 675 647.5 675 666.5 805 666.5 805 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 740 654.5 0 114 23 -input_fastq_read1_files ", fillcolor="#94DDF4", height=0.27778, label=input_fastq_read1_files, pos="740,657", rects="675,647.5,805,666.5", width=1.8056]; picard_jar_path [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1251 647.5 1251 666.5 1343 666.5 1343 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1297 654.5 0 76 15 -picard_jar_path ", fillcolor="#94DDF4", height=0.27778, label=picard_jar_path, pos="1297,657", rects="1251,647.5,1343,666.5", width=1.2778]; input_fastq_umi_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 486.5 647.5 486.5 666.5 607.5 666.5 607.5 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 547 654.5 0 105 21 -input_fastq_umi_files ", fillcolor="#94DDF4", height=0.27778, label=input_fastq_umi_files, pos="547,657", rects="486.5,647.5,607.5,666.5", width=1.6806]; genome_ref_first_index_file [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 330 647.5 330 666.5 482 666.5 482 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 406 654.5 0 136 27 -genome_ref_first_index_file ", fillcolor="#94DDF4", height=0.27778, label=genome_ref_first_index_file, pos="406,657", rects="330,647.5,482,666.5", width=2.1111]; ENCODE_blacklist_bedfile [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 909.5 647.5 909.5 666.5 1052.5 666.5 1052.5 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 981 654.5 0 127 24 -ENCODE_blacklist_bedfile ", fillcolor="#94DDF4", height=0.27778, label=ENCODE_blacklist_bedfile, pos="981,657", rects="909.5,647.5,1052.5,666.5", width=1.9861]; genome_sizes_file [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 84.5 647.5 84.5 666.5 191.5 666.5 191.5 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 138 654.5 0 91 17 -genome_sizes_file ", fillcolor="#94DDF4", height=0.27778, label=genome_sizes_file, pos="138,657", rects="84.5,647.5,191.5,666.5", width=1.4861]; } subgraph cluster_outputs { graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 151 8 151 82 1258 82 1258 8 ", _ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 205 15 0 92 16 -Workflow Outputs ", bb="151,8,1258,82", label="Workflow Outputs", labelloc=b, lheight=0.15, lp="205,17.5", lwidth=1.28, rank=same, style=dashed ]; output_preseq_c_curve_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 762.5 54.5 762.5 73.5 917.5 73.5 917.5 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 840 61.5 0 139 27 -output_preseq_c_curve_files ", fillcolor="#94DDF4", height=0.27778, label=output_preseq_c_curve_files, pos="840,64", rects="762.5,54.5,917.5,73.5", width=2.1528]; output_data_bam_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 922 54.5 922 73.5 1050 73.5 1050 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 986 61.5 0 112 21 -output_data_bam_files ", fillcolor="#94DDF4", height=0.27778, label=output_data_bam_files, pos="986,64", rects="922,54.5,1050,73.5", width=1.7778]; output_picard_mark_duplicates_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1054.5 54.5 1054.5 73.5 1249.5 73.5 1249.5 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1152 61.5 0 179 35 -output_picard_mark_duplicates_files ", fillcolor="#94DDF4", height=0.27778, label=output_picard_mark_duplicates_files, pos="1152,64", rects="1054.5,54.5,1249.5,73.5", width=2.7083]; output_data_unmapped_fastq_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 159 54.5 159 73.5 347 73.5 347 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 253 61.5 0 172 32 -output_data_unmapped_fastq_files ", fillcolor="#94DDF4", height=0.27778, label=output_data_unmapped_fastq_files, pos="253,64", rects="159,54.5,347,73.5", width=2.6111]; output_bowtie_log [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 351.5 54.5 351.5 73.5 458.5 73.5 458.5 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 405 61.5 0 91 17 -output_bowtie_log ", fillcolor="#94DDF4", height=0.27778, label=output_bowtie_log, pos="405,64", rects="351.5,54.5,458.5,73.5", width=1.4861]; output_data_dedup_bam_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 595.5 54.5 595.5 73.5 758.5 73.5 758.5 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 677 61.5 0 147 27 -output_data_dedup_bam_files ", fillcolor="#94DDF4", height=0.27778, label=output_data_dedup_bam_files, pos="677,64", rects="595.5,54.5,758.5,73.5", width=2.2639]; output_templates_files [_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 463 54.5 463 73.5 591 73.5 591 54.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 527 61.5 0 112 22 -output_templates_files ", fillcolor="#94DDF4", height=0.27778, label=output_templates_files, pos="527,64", rects="463,54.5,591,73.5", width=1.7778]; } sort_bams_by_tag_name [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 636.5 504.5 636.5 523.5 775.5 523.5 775.5 504.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 706 511.5 0 123 21 -sort_bams_by_tag_name ", height=0.27778, label=sort_bams_by_tag_name, pos="706,514", rects="636.5,504.5,775.5,523.5", width=1.9306]; nthreads -> sort_bams_by_tag_name [_draw_="c 7 -#000000 B 7 638.16 647.68 632.04 628.12 619.98 578.64 643 549 650.42 539.44 661.31 532.24 671.96 526.98 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 672.89 529.25 678.24 524.11 670.85 524.79 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 648.5 579.6 0 37 8 -nthreads ", label=nthreads, lp="648.5,581.5", pos="e,679.62,523.49 638.16,647.68 632.04,628.12 619.98,578.64 643,549 650.42,539.44 661.31,532.24 671.96,526.98"]; filter_quality_alignments [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 643 549.5 643 568.5 781 568.5 781 549.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 712 556.5 0 122 25 -filter_quality_alignments ", height=0.27778, label=filter_quality_alignments, pos="712,559", rects="643,549.5,781,568.5", width=1.9167]; nthreads -> filter_quality_alignments [_draw_="c 7 -#000000 B 7 651.51 647.62 672.35 630.89 717.26 594.23 721 586 722.42 582.86 722.33 579.42 721.46 576.11 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 723.74 575.2 718.72 569.74 719.24 577.14 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 732.5 602.1 0 37 8 -nthreads ", label=nthreads, lp="732.5,604", pos="e,718.12,568.35 651.51,647.62 672.35,630.89 717.26,594.23 721,586 722.42,582.86 722.33,579.42 721.46,576.11"]; sort_masked_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 755.5 414.5 755.5 433.5 866.5 433.5 866.5 414.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 811 421.5 0 95 16 -sort_masked_bams ", height=0.27778, label=sort_masked_bams, pos="811,424", rects="755.5,414.5,866.5,433.5", width=1.5417]; nthreads -> sort_masked_bams [_draw_="c 7 -#000000 B 13 655.48 647.55 661.37 644.44 668.34 641.15 675 639 724.9 622.86 788 657.45 788 605 788 605 788 605 788 468 788 \ 457.76 793.14 447.59 798.55 439.72 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 800.3 441.47 802.56 434.41 796.39 438.52 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 806.5 534.6 0 37 8 -nthreads ", label=nthreads, lp="806.5,536.5", pos="e,803.47,433.2 655.48,647.55 661.37,644.44 668.34,641.15 675,639 724.9,622.86 788,657.45 788,605 788,605 788,605 788,468 788,457.76 \ 793.14,447.59 798.55,439.72"]; bowtie2 [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 377 594.5 377 613.5 433 613.5 433 594.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 405 601.5 0 40 7 -bowtie2 ", height=0.27778, label=bowtie2, pos="405,604", rects="377,594.5,433,613.5", width=0.77778]; nthreads -> bowtie2 [_draw_="c 7 -#000000 B 13 627.34 647.56 621.57 644.38 614.66 641.03 608 639 578.9 630.11 569.52 638.38 540 631 529.35 628.34 527.6 624.84 \ 517 622 492.18 615.35 463.52 611.06 441.41 608.45 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 441.7 606.02 434.47 607.67 441.16 610.89 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 558.5 624.6 0 37 8 -nthreads ", label=nthreads, lp="558.5,626.5", pos="e,432.97,607.5 627.34,647.56 621.57,644.38 614.66,641.03 608,639 578.9,630.11 569.52,638.38 540,631 529.35,628.34 527.6,624.84 517,\ 622 492.18,615.35 463.52,611.06 441.41,608.45"]; sort_dedup_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 612.5 144.5 612.5 163.5 715.5 163.5 715.5 144.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 664 151.5 0 87 15 -sort_dedup_bams ", height=0.27778, label=sort_dedup_bams, pos="664,154", rects="612.5,144.5,715.5,163.5", width=1.4306]; nthreads -> sort_dedup_bams [_draw_="c 7 -#000000 B 13 637.5 647.81 635.59 643 633.34 636.75 632 631 624.8 600.07 624 591.76 624 560 624 560 624 560 624 198 624 185.86 \ 632.66 175.71 641.92 168.32 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 643.19 170.42 647.42 164.33 640.32 166.45 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 642.5 399.6 0 37 8 -nthreads ", label=nthreads, lp="642.5,401.5", pos="e,648.65,163.44 637.5,647.81 635.59,643 633.34,636.75 632,631 624.8,600.07 624,591.76 624,560 624,560 624,560 624,198 624,185.86 \ 632.66,175.71 641.92,168.32"]; sort_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 492 549.5 492 568.5 560 568.5 560 549.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 526 556.5 0 52 9 -sort_bams ", height=0.27778, label=sort_bams, pos="526,559", rects="492,549.5,560,568.5", width=0.94444]; nthreads -> sort_bams [_draw_="c 7 -#000000 B 7 628.91 647.7 617.16 639.49 598.95 626.4 584 614 568.45 601.11 551.66 585.24 540.17 574.05 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 542.16 572.58 535.45 569.43 538.73 576.08 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 602.5 602.1 0 37 8 -nthreads ", label=nthreads, lp="602.5,604", pos="e,534.37,568.37 628.91,647.7 617.16,639.49 598.95,626.4 584,614 568.45,601.11 551.66,585.24 540.17,574.05"]; annotate_bams_with_umis [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1008 324.5 1008 343.5 1156 343.5 1156 324.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1082 331.5 0 132 23 -annotate_bams_with_umis ", height=0.27778, label=annotate_bams_with_umis, pos="1082,334", rects="1008,324.5,1156,343.5", width=2.0556]; picard_java_opts -> annotate_bams_with_umis [_draw_="c 7 -#000000 B 10 1181.02 647.58 1167.05 638.95 1149 624.09 1149 605 1149 605 1149 605 1149 378 1149 363.19 1137.26 353.24 1123.61 \ 346.69 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1124.68 344.48 1117.28 343.98 1122.75 348.98 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1169 489.6 0 40 9 -java_opts ", label=java_opts, lp="1169,491.5", pos="e,1115.9,343.38 1181,647.58 1167.1,638.95 1149,624.09 1149,605 1149,605 1149,605 1149,378 1149,363.19 1137.3,353.24 1123.6,346.69"]; mark_duplicates [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1103 279.5 1103 298.5 1201 298.5 1201 279.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1152 286.5 0 82 15 -mark_duplicates ", height=0.27778, label=mark_duplicates, pos="1152,289", rects="1103,279.5,1201,298.5", width=1.3611]; picard_java_opts -> mark_duplicates [_draw_="c 7 -#000000 B 10 1197 647.7 1197 637.6 1197 620.05 1197 605 1197 605 1197 605 1197 333 1197 320.27 1187.47 310.15 1177.18 302.93 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1178.55 300.9 1171.32 299.22 1175.92 305.03 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1217 467.1 0 40 9 -java_opts ", label=java_opts, lp="1217,469", pos="e,1170,298.4 1197,647.7 1197,637.6 1197,620.05 1197,605 1197,605 1197,605 1197,333 1197,320.27 1187.5,310.15 1177.2,302.93"]; fgbio_jar_path -> annotate_bams_with_umis [_draw_="c 7 -#000000 B 10 1095.08 647.66 1089.75 637.81 1082 620.77 1082 605 1082 605 1082 605 1082 378 1082 369.31 1082 359.63 1082 351.65 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1084.45 351.76 1082 344.76 1079.55 351.76 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1111 489.6 0 58 14 -fgbio_jar_path ", label=fgbio_jar_path, lp="1111,491.5", pos="e,1082,343.24 1095.1,647.66 1089.8,637.81 1082,620.77 1082,605 1082,605 1082,605 1082,378 1082,369.31 1082,359.63 1082,351.65"]; input_fastq_read2_files -> bowtie2 [_draw_="c 7 -#000000 B 7 271.07 647.65 281.08 639.8 297.18 628.34 313 622 330.75 614.89 351.64 610.73 369.01 608.3 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 369.1 610.76 375.73 607.44 368.48 605.9 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 358.5 624.6 0 91 22 -input_fastq_read2_file ", label=input_fastq_read2_file, lp="358.5,626.5", pos="e,377.23,607.24 271.07,647.65 281.08,639.8 297.18,628.34 313,622 330.75,614.89 351.64,610.73 369.01,608.3"]; regions_bed_file -> filter_quality_alignments [_draw_="c 7 -#000000 B 7 874.98 647.62 897.68 635.93 931.86 613.91 915 594 898.82 574.88 839.48 566.51 789.1 562.84 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 789.44 560.41 782.29 562.37 789.11 565.3 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 921.5 602.1 0 5 1 -L ", label=L, lp="921.5,604", pos="e,780.78,562.27 874.98,647.62 897.68,635.93 931.86,613.91 915,594 898.82,574.88 839.48,566.51 789.1,562.84"]; basename [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 0 647.5 0 666.5 68 666.5 68 647.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 34 654.5 0 52 8 -basename ", height=0.27778, label=basename, pos="34,657", rects="0,647.5,68,666.5", width=0.94444]; input_fastq_read1_files -> basename [_draw_="c 7 -#000000 B 10 732.26 666.3 720.59 679.5 697.06 703.1 671 712.25 639.76 723.22 104.58 727.13 75 712.25 59.1 704.25 47.81 686.83 \ 41.16 673.68 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 43.46 672.82 38.26 667.53 39.03 674.91 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 371 723.6 0 36 9 -file_path ", label=file_path, lp="371,725.5", pos="e,37.617,666.16 732.26,666.3 720.59,679.5 697.06,703.1 671,712.25 639.76,723.22 104.58,727.13 75,712.25 59.095,704.25 47.811,686.83 \ 41.16,673.68"]; input_fastq_read1_files -> bowtie2 [_draw_="c 7 -#000000 B 10 707.45 647.55 695.97 644.68 682.94 641.56 671 639 629.92 630.19 619.61 627.84 578 622 531.02 615.41 476.52 610.5 \ 441.43 607.7 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 441.63 605.26 434.46 607.15 441.25 610.14 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 677.5 624.6 0 91 22 -input_fastq_read1_file ", label=input_fastq_read1_file, lp="677.5,626.5", pos="e,432.95,607.03 707.45,647.55 695.97,644.68 682.94,641.56 671,639 629.92,630.19 619.61,627.84 578,622 531.02,615.41 476.52,610.5 \ 441.43,607.7"]; extract_basename_1 [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 795.5 594.5 795.5 613.5 914.5 613.5 914.5 594.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 855 601.5 0 103 18 -extract_basename_1 ", height=0.27778, label=extract_basename_1, pos="855,604", rects="795.5,594.5,914.5,613.5", width=1.6528]; input_fastq_read1_files -> extract_basename_1 [_draw_="c 7 -#000000 B 4 758.99 647.58 777.88 639.2 807.04 626.27 828.27 616.85 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 829.19 619.13 834.6 614.05 827.21 614.65 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 833 624.6 0 38 10 -input_file ", label=input_file, lp="833,626.5", pos="e,835.98,613.43 758.99,647.58 777.88,639.2 807.04,626.27 828.27,616.85"]; picard_jar_path -> mark_duplicates [_draw_="c 7 -#000000 B 10 1289.62 647.64 1281.93 638.04 1271 621.5 1271 605 1271 605 1271 605 1271 333 1271 318.53 1239.49 307.57 1208.9 \ 300.33 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1209.59 297.98 1202.22 298.82 1208.51 302.76 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1302.5 467.1 0 63 15 -picard_jar_path ", label=picard_jar_path, lp="1302.5,469", pos="e,1200.7,298.48 1289.6,647.64 1281.9,638.04 1271,621.5 1271,605 1271,605 1271,605 1271,333 1271,318.53 1239.5,307.57 1208.9,300.33"]; input_fastq_umi_files -> annotate_bams_with_umis [_draw_="c 7 -#000000 B 10 553.38 647.6 556.67 642.93 560.5 636.88 563 631 604.85 532.59 542.47 471.69 619 397 645.76 370.88 874.32 350.21 \ 999.99 340.7 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 999.81 343.17 1006.6 340.2 999.44 338.29 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 589 489.6 0 22 5 -fastq ", label=fastq, lp="589,491.5", pos="e,1008.1,340.09 553.38,647.6 556.67,642.93 560.5,636.88 563,631 604.85,532.59 542.47,471.69 619,397 645.76,370.88 874.32,350.21 \ 999.99,340.7"]; genome_ref_first_index_file -> bowtie2 [_draw_="c 7 -#000000 B 4 405.83 647.58 405.7 640.52 405.49 630.24 405.32 621.55 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 407.78 621.73 405.19 614.78 402.88 621.82 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 460.5 624.6 0 111 27 -genome_ref_first_index_file ", label=genome_ref_first_index_file, lp="460.5,626.5", pos="e,405.16,613.26 405.83,647.58 405.7,640.52 405.49,630.24 405.32,621.55"]; remove_encode_blacklist [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 795.5 459.5 795.5 478.5 936.5 478.5 936.5 459.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 866 466.5 0 125 23 -remove_encode_blacklist ", height=0.27778, label=remove_encode_blacklist, pos="866,469", rects="795.5,459.5,936.5,478.5", width=1.9583]; ENCODE_blacklist_bedfile -> remove_encode_blacklist [_draw_="c 7 -#000000 B 10 982.31 647.72 983.8 637.65 986 620.12 986 605 986 605 986 605 986 513 986 498.47 954.45 487.54 923.7 480.33 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 924.34 477.97 916.98 478.82 923.27 482.75 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 995.5 557.1 0 19 5 -bFile ", label=bFile, lp="995.5,559", pos="e,915.5,478.49 982.31,647.72 983.8,637.65 986,620.12 986,605 986,605 986,605 986,513 986,498.47 954.45,487.54 923.7,480.33"]; index_masked_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 751.5 369.5 751.5 388.5 870.5 388.5 870.5 369.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 811 376.5 0 103 17 -index_masked_bams ", height=0.27778, label=index_masked_bams, pos="811,379", rects="751.5,369.5,870.5,388.5", width=1.6528]; "preseq-c-curve" [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 751.5 99.5 751.5 118.5 840.5 118.5 840.5 99.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 796 106.5 0 73 14 -preseq-c-curve ", height=0.27778, label="preseq-c-curve", pos="796,109", rects="751.5,99.5,840.5,118.5", width=1.2361]; index_masked_bams -> "preseq-c-curve" [_draw_="c 7 -#000000 B 10 755.77 369.58 738.09 363.49 723 353.02 723 335 723 335 723 335 723 153 723 137.84 734.83 127.92 748.96 121.48 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 749.54 123.88 755.11 118.98 747.7 119.34 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 757 242.1 0 68 17 -input_sorted_file ", label=input_sorted_file, lp="757,244", pos="e,756.51,118.41 755.77,369.58 738.09,363.49 723,353.02 723,335 723,335 723,335 723,153 723,137.84 734.83,127.92 748.96,121.48"]; index_masked_bams -> annotate_bams_with_umis [_draw_="c 7 -#000000 B 4 864.54 369.5 909.36 362.39 973.34 352.24 1020.3 344.79 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1020.55 347.23 1027.08 343.71 1019.78 342.39 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 981 354.6 0 22 5 -input ", label=input, lp="981,356.5", pos="e,1028.6,343.48 864.54,369.5 909.36,362.39 973.34,352.24 1020.3,344.79"]; bam_to_bepe [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 632.5 189.5 632.5 208.5 715.5 208.5 715.5 189.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 674 196.5 0 67 11 -bam_to_bepe ", height=0.27778, label=bam_to_bepe, pos="674,199", rects="632.5,189.5,715.5,208.5", width=1.1528]; cut_to_bepe [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 531 144.5 531 163.5 607 163.5 607 144.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 569 151.5 0 60 11 -cut_to_bepe ", height=0.27778, label=cut_to_bepe, pos="569,154", rects="531,144.5,607,163.5", width=1.0556]; bam_to_bepe -> cut_to_bepe [_draw_="c 7 -#000000 B 7 649.48 189.52 642.2 186.9 634.24 183.93 627 181 616.26 176.66 604.58 171.51 594.54 166.94 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 595.64 164.75 588.25 164.06 593.6 169.2 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 646 174.6 0 38 10 -input_file ", label=input_file, lp="646,176.5", pos="e,586.88,163.43 649.48,189.52 642.2,186.9 634.24,183.93 627,181 616.26,176.66 604.58,171.51 594.54,166.94"]; extract_basename_2 [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 858.5 549.5 858.5 568.5 977.5 568.5 977.5 549.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 918 556.5 0 103 18 -extract_basename_2 ", height=0.27778, label=extract_basename_2, pos="918,559", rects="858.5,549.5,977.5,568.5", width=1.6528]; index_dups_marked_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 913 234.5 913 253.5 1059 253.5 1059 234.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 986 241.5 0 130 22 -index_dups_marked_bams ", height=0.27778, label=index_dups_marked_bams, pos="986,244", rects="913,234.5,1059,253.5", width=2.0278]; index_dups_marked_bams -> output_data_bam_files [_draw_="c 7 -#000000 B 10 986 234.76 986 226.1 986 212.09 986 200 986 200 986 200 986 108 986 99.31 986 89.63 986 81.65 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 988.45 81.76 986 74.76 983.55 81.76 ", pos="e,986,73.243 986,234.76 986,226.1 986,212.09 986,200 986,200 986,200 986,108 986,99.308 986,89.627 986,81.655"]; remove_duplicates [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 806 189.5 806 208.5 916 208.5 916 189.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 861 196.5 0 94 17 -remove_duplicates ", height=0.27778, label=remove_duplicates, pos="861,199", rects="806,189.5,916,208.5", width=1.5278]; index_dups_marked_bams -> remove_duplicates [_draw_="c 7 -#000000 B 4 961.3 234.5 941.87 227.82 914.63 218.45 893.44 211.16 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 894.49 208.93 887.08 208.97 892.9 213.56 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 953 219.6 0 38 10 -input_file ", label=input_file, lp="953,221.5", pos="e,885.64,208.48 961.3,234.5 941.87,227.82 914.63,218.45 893.44,211.16"]; "preseq-c-curve" -> output_preseq_c_curve_files [_draw_="c 7 -#000000 B 4 804.48 99.71 810.45 93.88 818.58 85.93 825.56 79.12 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 827.17 80.97 830.46 74.32 823.74 77.46 ", pos="e,831.54,73.265 804.48,99.709 810.45,93.879 818.58,85.934 825.56,79.117"]; sort_bams_by_tag_name -> bam_to_bepe [_draw_="c 7 -#000000 B 10 698.47 504.8 691.76 496.62 683 483.38 683 470 683 470 683 470 683 243 683 234.13 681.14 224.45 679.12 216.53 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 681.51 215.99 677.26 209.91 676.8 217.32 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 692.5 354.6 0 19 3 -bam ", label=bam, lp="692.5,356.5", pos="e,676.85,208.46 698.47,504.8 691.76,496.62 683,483.38 683,470 683,470 683,470 683,243 683,234.13 681.14,224.45 679.12,216.53"]; sort_bams_by_tag_name -> remove_encode_blacklist [_draw_="c 7 -#000000 B 4 737.61 504.5 763.03 497.67 798.89 488.03 826.26 480.68 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 826.87 483.05 832.99 478.87 825.6 478.32 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 812 489.6 0 24 4 -abam ", label=abam, lp="812,491.5", pos="e,834.45,478.48 737.61,504.5 763.03,497.67 798.89,488.03 826.26,480.68"]; basename -> bowtie2 [_draw_="c 7 -#000000 B 7 52.08 647.59 59.12 644.55 67.33 641.31 75 639 178.48 607.78 307.59 604.06 369.14 604.3 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 368.84 606.75 375.85 604.35 368.87 601.85 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 155.5 624.6 0 21 4 -ungz ", label=ungz, lp="155.5,626.5", pos="e,377.37,604.36 52.084,647.59 59.123,644.55 67.328,641.31 75,639 178.48,607.78 307.59,604.06 369.14,604.3"]; basename -> bowtie2 [_draw_="c 7 -#000000 B 13 51.16 647.51 58.36 644.31 66.92 640.98 75 639 114.87 629.25 126.24 635.78 167 631 194.22 627.81 200.8 625.31 228 \ 622 276.65 616.08 333.04 610.96 368.85 607.93 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 368.78 610.4 375.55 607.37 368.37 605.51 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 261.5 624.6 0 67 15 -output_filename ", label=output_filename, lp="261.5,626.5", pos="e,377.06,607.24 51.16,647.51 58.356,644.31 66.916,640.98 75,639 114.87,629.25 126.24,635.78 167,631 194.22,627.81 200.8,625.31 228,\ 622 276.65,616.08 333.04,610.96 368.85,607.93"]; remove_duplicates -> sort_dedup_bams [_draw_="c 7 -#000000 B 4 822.08 189.5 790.11 182.53 744.72 172.62 710.77 165.21 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 711.68 162.9 704.32 163.8 710.64 167.69 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 799 174.6 0 38 10 -input_file ", label=input_file, lp="799,176.5", pos="e,702.84,163.48 822.08,189.5 790.11,182.53 744.72,172.62 710.77,165.21"]; filter_quality_alignments -> sort_bams_by_tag_name [_draw_="c 7 -#000000 B 4 710.84 549.71 710.13 544.59 709.19 537.85 708.33 531.67 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 710.76 531.36 707.36 524.76 705.9 532.04 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 728 534.6 0 38 10 -input_file ", label=input_file, lp="728,536.5", pos="e,707.15,523.27 710.84,549.71 710.13,544.59 709.19,537.85 708.33,531.67"]; remove_encode_blacklist -> sort_masked_bams [_draw_="c 7 -#000000 B 4 855.13 459.5 847.53 453.56 837.2 445.48 828.44 438.64 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 830.06 436.79 823.04 434.41 827.04 440.65 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 862 444.6 0 38 10 -input_file ", label=input_file, lp="862,446.5", pos="e,821.84,433.48 855.13,459.5 847.53,453.56 837.2,445.48 828.44,438.64"]; sort_masked_bams -> index_masked_bams [_draw_="c 7 -#000000 B 4 811 414.71 811 409.59 811 402.85 811 396.67 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 813.45 396.78 811 389.78 808.55 396.78 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 830 399.6 0 38 10 -input_file ", label=input_file, lp="830,401.5", pos="e,811,388.27 811,414.71 811,409.59 811,402.85 811,396.67"]; annotate_bams_with_umis -> mark_duplicates [_draw_="c 7 -#000000 B 4 1095.83 324.5 1105.9 318.32 1119.71 309.84 1131.11 302.83 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1132.23 305.02 1136.91 299.27 1129.66 300.85 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1142 309.6 0 38 10 -input_file ", label=input_file, lp="1142,311.5", pos="e,1138.2,298.48 1095.8,324.5 1105.9,318.32 1119.7,309.84 1131.1,302.83"]; index_dedup_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 618.5 99.5 618.5 118.5 729.5 118.5 729.5 99.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 674 106.5 0 95 16 -index_dedup_bams ", height=0.27778, label=index_dedup_bams, pos="674,109", rects="618.5,99.5,729.5,118.5", width=1.5417]; index_dedup_bams -> output_data_dedup_bam_files [_draw_="c 7 -#000000 B 4 674.58 99.71 674.94 94.59 675.41 87.85 675.84 81.67 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 678.27 81.93 676.32 74.78 673.39 81.59 ", pos="e,676.42,73.265 674.58,99.709 674.94,94.593 675.41,87.848 675.84,81.666"]; sort_to_bepe [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 514 99.5 514 118.5 594 118.5 594 99.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 554 106.5 0 64 12 -sort_to_bepe ", height=0.27778, label=sort_to_bepe, pos="554,109", rects="514,99.5,594,118.5", width=1.1111]; cut_to_bepe -> sort_to_bepe [_draw_="c 7 -#000000 B 4 566.11 144.71 564.28 139.47 561.86 132.53 559.66 126.24 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 562 125.5 557.38 119.69 557.37 127.11 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 581 129.6 0 38 10 -input_file ", label=input_file, lp="581,131.5", pos="e,556.88,118.27 566.11,144.71 564.28,139.47 561.86,132.53 559.66,126.24"]; bowtie2 -> output_data_unmapped_fastq_files [_draw_="c 7 -#000000 B 10 377.12 599.73 353.69 595.24 324 584.68 324 560 324 560 324 560 324 108 324 92.91 312.11 82.96 298.07 76.49 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 299.38 74.38 291.98 73.98 297.52 78.91 ", pos="e,290.58,73.406 377.12,599.73 353.69,595.24 324,584.68 324,560 324,560 324,560 324,108 324,92.906 312.11,82.965 298.07,76.487"]; bowtie2 -> output_bowtie_log [_draw_="c 7 -#000000 B 10 405 594.76 405 586.1 405 572.09 405 560 405 560 405 560 405 108 405 99.31 405 89.63 405 81.65 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 407.45 81.76 405 74.76 402.55 81.76 ", pos="e,405,73.243 405,594.76 405,586.1 405,572.09 405,560 405,560 405,560 405,108 405,99.308 405,89.627 405,81.655"]; bowtie2 -> filter_quality_alignments [_draw_="c 7 -#000000 B 10 432.6 601.46 500.09 597.68 668.39 588.07 674 586 680.25 583.69 680.54 580.83 686 577 687.9 575.67 689.91 574.3 \ 691.92 572.95 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 692.91 575.22 697.4 569.32 690.21 571.14 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 705 579.6 0 38 10 -input_file ", label=input_file, lp="705,581.5", pos="e,698.66,568.49 432.6,601.46 500.09,597.68 668.39,588.07 674,586 680.25,583.69 680.54,580.83 686,577 687.9,575.67 689.91,574.3 691.92,\ 572.95"]; bowtie2 -> sort_bams [_draw_="c 7 -#000000 B 4 428.91 594.5 447.63 587.85 473.85 578.53 494.33 571.26 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 494.94 573.64 500.72 568.98 493.3 569.02 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 495 579.6 0 38 10 -input_file ", label=input_file, lp="495,581.5", pos="e,502.14,568.48 428.91,594.5 447.63,587.85 473.85,578.53 494.33,571.26"]; sort_dedup_bams -> index_dedup_bams [_draw_="c 7 -#000000 B 4 665.93 144.71 667.15 139.47 668.76 132.53 670.22 126.24 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 672.54 127.11 671.73 119.74 667.76 126 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 688 129.6 0 38 10 -input_file ", label=input_file, lp="688,131.5", pos="e,672.08,118.27 665.93,144.71 667.15,139.47 668.76,132.53 670.22,126.24"]; index_bams [_draw_="c 7 -#000000 C 7 -#fafad2 P 4 488 504.5 488 523.5 564 523.5 564 504.5 ", _ldraw_="F 10 9 -Helvetica c 7 -#000000 T 526 511.5 0 60 10 -index_bams ", height=0.27778, label=index_bams, pos="526,514", rects="488,504.5,564,523.5", width=1.0556]; sort_bams -> index_bams [_draw_="c 7 -#000000 B 4 526 549.71 526 544.59 526 537.85 526 531.67 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 528.45 531.78 526 524.78 523.55 531.78 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 545 534.6 0 38 10 -input_file ", label=input_file, lp="545,536.5", pos="e,526,523.27 526,549.71 526,544.59 526,537.85 526,531.67"]; sort_to_bepe -> output_templates_files [_draw_="c 7 -#000000 B 4 548.79 99.71 545.36 94.24 540.75 86.9 536.66 80.38 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 538.79 79.17 532.99 74.55 534.64 81.78 ", pos="e,532.19,73.265 548.79,99.709 545.36,94.236 540.75,86.899 536.66,80.381"]; mark_duplicates -> output_picard_mark_duplicates_files [_draw_="c 7 -#000000 B 10 1152 279.76 1152 271.1 1152 257.09 1152 245 1152 245 1152 245 1152 108 1152 99.31 1152 89.63 1152 81.65 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1154.45 81.76 1152 74.76 1149.55 81.76 ", pos="e,1152,73.243 1152,279.76 1152,271.1 1152,257.09 1152,245 1152,245 1152,245 1152,108 1152,99.308 1152,89.627 1152,81.655"]; mark_duplicates -> index_dups_marked_bams [_draw_="c 7 -#000000 B 4 1119.2 279.5 1092.72 272.64 1055.3 262.95 1026.87 255.59 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1027.58 253.24 1020.19 253.86 1026.36 257.98 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1102 264.6 0 38 10 -input_file ", label=input_file, lp="1102,266.5", pos="e,1018.7,253.48 1119.2,279.5 1092.7,272.64 1055.3,262.95 1026.9,255.59"]; extract_basename_1 -> extract_basename_2 [_draw_="c 7 -#000000 B 4 867.45 594.5 876.33 588.44 888.46 580.16 898.61 573.23 ", _hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 899.93 575.3 904.33 569.33 897.17 571.25 ", _ldraw_="F 8 9 -Helvetica c 7 -#000000 T 910 579.6 0 36 9 -file_path ", label=file_path, lp="910,581.5", pos="e,905.58,568.48 867.45,594.5 876.33,588.44 888.46,580.16 898.61,573.23"]; }