rule_graph.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<!-- 0 -->
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<!-- 1 -->
<g id="node2" class="node"><title>1</title>
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<!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge"><title>1&#45;&gt;0</title>
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<!-- 2 -->
<g id="node3" class="node"><title>2</title>
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<!-- 2&#45;&gt;1 -->
<g id="edge2" class="edge"><title>2&#45;&gt;1</title>
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<!-- 3 -->
<g id="node4" class="node"><title>3</title>
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<text text-anchor="middle" x="324" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
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<!-- 3&#45;&gt;2 -->
<g id="edge3" class="edge"><title>3&#45;&gt;2</title>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="39" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge7" class="edge"><title>4&#45;&gt;3</title>
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<!-- 5 -->
<g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="114" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 5&#45;&gt;3 -->
<g id="edge13" class="edge"><title>5&#45;&gt;3</title>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
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<text text-anchor="middle" x="83" y="-663.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 6&#45;&gt;3 -->
<g id="edge10" class="edge"><title>6&#45;&gt;3</title>
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<!-- 7 -->
<g id="node8" class="node"><title>7</title>
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<!-- 7&#45;&gt;3 -->
<g id="edge5" class="edge"><title>7&#45;&gt;3</title>
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<!-- 8 -->
<g id="node9" class="node"><title>8</title>
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<text text-anchor="middle" x="478" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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<!-- 8&#45;&gt;3 -->
<g id="edge8" class="edge"><title>8&#45;&gt;3</title>
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<!-- 9 -->
<g id="node10" class="node"><title>9</title>
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<text text-anchor="middle" x="303" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
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<!-- 9&#45;&gt;3 -->
<g id="edge9" class="edge"><title>9&#45;&gt;3</title>
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<!-- 10 -->
<g id="node11" class="node"><title>10</title>
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<text text-anchor="middle" x="467" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
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<!-- 10&#45;&gt;3 -->
<g id="edge4" class="edge"><title>10&#45;&gt;3</title>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
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<text text-anchor="middle" x="851" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 11&#45;&gt;3 -->
<g id="edge11" class="edge"><title>11&#45;&gt;3</title>
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<!-- 23 -->
<g id="node24" class="node"><title>23</title>
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<text text-anchor="middle" x="850" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<!-- 11&#45;&gt;23 -->
<g id="edge43" class="edge"><title>11&#45;&gt;23</title>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="835" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
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<!-- 12&#45;&gt;3 -->
<g id="edge12" class="edge"><title>12&#45;&gt;3</title>
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<!-- 13 -->
<g id="node14" class="node"><title>13</title>
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<text text-anchor="middle" x="806" y="-303.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
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<!-- 12&#45;&gt;13 -->
<g id="edge28" class="edge"><title>12&#45;&gt;13</title>
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<!-- 13&#45;&gt;3 -->
<g id="edge6" class="edge"><title>13&#45;&gt;3</title>
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<!-- 14 -->
<g id="node15" class="node"><title>14</title>
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<text text-anchor="middle" x="339" y="-735.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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<!-- 14&#45;&gt;6 -->
<g id="edge15" class="edge"><title>14&#45;&gt;6</title>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
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<text text-anchor="middle" x="416" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 14&#45;&gt;18 -->
<g id="edge34" class="edge"><title>14&#45;&gt;18</title>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
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<!-- 14&#45;&gt;20 -->
<g id="edge38" class="edge"><title>14&#45;&gt;20</title>
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<!-- 15 -->
<g id="node16" class="node"><title>15</title>
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<!-- 15&#45;&gt;6 -->
<g id="edge14" class="edge"><title>15&#45;&gt;6</title>
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<!-- 15&#45;&gt;7 -->
<g id="edge16" class="edge"><title>15&#45;&gt;7</title>
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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
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<!-- 16&#45;&gt;7 -->
<g id="edge17" class="edge"><title>16&#45;&gt;7</title>
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<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<!-- 16&#45;&gt;19 -->
<g id="edge36" class="edge"><title>16&#45;&gt;19</title>
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<!-- 22 -->
<g id="node23" class="node"><title>22</title>
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<!-- 16&#45;&gt;22 -->
<g id="edge42" class="edge"><title>16&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M673.279,-728.113C731.011,-719.162 820.701,-704.115 907.607,-683.955"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-687.357 917.367,-681.666 906.832,-680.542 908.43,-687.357"/>
</g>
<!-- 17 -->
<g id="node18" class="node"><title>17</title>
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<text text-anchor="middle" x="539" y="-447.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
<!-- 17&#45;&gt;8 -->
<g id="edge18" class="edge"><title>17&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-431.697C516.608,-423.305 507.69,-413.07 499.665,-403.861"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-401.344 492.905,-396.104 496.836,-405.943 502.114,-401.344"/>
</g>
<!-- 18&#45;&gt;9 -->
<g id="edge20" class="edge"><title>18&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-647.876C373.582,-638.724 355.209,-627.342 339.297,-617.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-614.481 330.749,-612.19 337.407,-620.431 341.093,-614.481"/>
</g>
<!-- 18&#45;&gt;10 -->
<g id="edge22" class="edge"><title>18&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-647.697C434.597,-639.474 441.876,-629.483 448.479,-620.421"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-622.248 454.538,-612.104 445.821,-618.126 451.478,-622.248"/>
</g>
<!-- 19&#45;&gt;9 -->
<g id="edge19" class="edge"><title>19&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-649.378C460.723,-639.163 412.756,-625.732 373.621,-614.774"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-611.371 363.874,-612.045 372.56,-618.111 374.447,-611.371"/>
</g>
<!-- 19&#45;&gt;10 -->
<g id="edge21" class="edge"><title>19&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-647.697C520.911,-638.881 507.582,-628.032 495.84,-618.474"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-615.703 488.014,-612.104 493.56,-621.132 497.979,-615.703"/>
</g>
<!-- 20&#45;&gt;11 -->
<g id="edge24" class="edge"><title>20&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-649.313C918.045,-641.265 936.359,-629.365 947,-612 955.359,-598.357 955.132,-589.779 947,-576 934.386,-554.628 909.727,-541.279 888.56,-533.324"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="889.422,-529.918 878.828,-529.94 887.123,-536.53 889.422,-529.918"/>
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<!-- 21 -->
<g id="node22" class="node"><title>21</title>
<path fill="none" stroke="#56b9d8" stroke-width="2" d="M926,-612C926,-612 776,-612 776,-612 770,-612 764,-606 764,-600 764,-600 764,-588 764,-588 764,-582 770,-576 776,-576 776,-576 926,-576 926,-576 932,-576 938,-582 938,-588 938,-588 938,-600 938,-600 938,-606 932,-612 926,-612"/>
<text text-anchor="middle" x="851" y="-591.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 20&#45;&gt;21 -->
<g id="edge40" class="edge"><title>20&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-647.697C845.859,-639.983 846.919,-630.712 847.901,-622.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-622.437 849.045,-612.104 844.432,-621.642 851.387,-622.437"/>
</g>
<!-- 28 -->
<g id="node29" class="node"><title>28</title>
<path fill="none" stroke="#d8b456" stroke-width="2" d="M780,-540C780,-540 692,-540 692,-540 686,-540 680,-534 680,-528 680,-528 680,-516 680,-516 680,-510 686,-504 692,-504 692,-504 780,-504 780,-504 786,-504 792,-510 792,-516 792,-516 792,-528 792,-528 792,-534 786,-540 780,-540"/>
<text text-anchor="middle" x="736" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 20&#45;&gt;28 -->
<g id="edge46" class="edge"><title>20&#45;&gt;28</title>
<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-647.827C783.272,-639.345 766.08,-627.537 755,-612 742.133,-593.959 737.662,-568.972 736.249,-550.065"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="739.741,-549.812 735.737,-540.002 732.75,-550.167 739.741,-549.812"/>
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<!-- 21&#45;&gt;11 -->
<g id="edge23" class="edge"><title>21&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M851,-575.697C851,-567.983 851,-558.712 851,-550.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-550.104 851,-540.104 847.5,-550.104 854.5,-550.104"/>
</g>
<!-- 21&#45;&gt;28 -->
<g id="edge45" class="edge"><title>21&#45;&gt;28</title>
<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-575.876C807.832,-566.724 789.133,-555.342 772.94,-545.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-542.4 764.24,-540.19 770.962,-548.379 774.602,-542.4"/>
</g>
<!-- 22&#45;&gt;11 -->
<g id="edge25" class="edge"><title>22&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-647.724C975.205,-628.573 978.916,-597.548 965,-576 948.17,-549.94 914.888,-536.48 888.609,-529.662"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-526.183 878.57,-527.284 887.494,-532.994 889.107,-526.183"/>
</g>
<!-- 22&#45;&gt;21 -->
<g id="edge39" class="edge"><title>22&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-647.876C922.832,-638.724 904.133,-627.342 887.94,-617.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-614.4 879.24,-612.19 885.962,-620.379 889.602,-614.4"/>
</g>
<!-- 22&#45;&gt;28 -->
<g id="edge48" class="edge"><title>22&#45;&gt;28</title>
<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-647.807C967.882,-627.847 965.54,-595.215 947,-576 941.799,-570.609 861.991,-551.541 802.055,-537.821"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="802.775,-534.395 792.247,-535.582 801.217,-541.22 802.775,-534.395"/>
</g>
<!-- 23&#45;&gt;12 -->
<g id="edge27" class="edge"><title>23&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-431.697C844.639,-423.983 842.653,-414.712 840.81,-406.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-405.149 838.665,-396.104 837.338,-406.616 844.183,-405.149"/>
</g>
<!-- 24 -->
<g id="node25" class="node"><title>24</title>
<path fill="none" stroke="#b6d856" stroke-width="2" d="M1054,-540C1054,-540 974,-540 974,-540 968,-540 962,-534 962,-528 962,-528 962,-516 962,-516 962,-510 968,-504 974,-504 974,-504 1054,-504 1054,-504 1060,-504 1066,-510 1066,-516 1066,-516 1066,-528 1066,-528 1066,-534 1060,-540 1054,-540"/>
<text text-anchor="middle" x="1014" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
<!-- 24&#45;&gt;12 -->
<g id="edge26" class="edge"><title>24&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-503.668C981.776,-484.746 952.678,-454.186 924,-432 907.558,-419.28 887.819,-407.241 871.112,-397.862"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="872.629,-394.702 862.182,-392.937 869.249,-400.831 872.629,-394.702"/>
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<!-- 25 -->
<g id="node26" class="node"><title>25</title>
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<text text-anchor="middle" x="344" y="-807.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 25&#45;&gt;14 -->
<g id="edge29" class="edge"><title>25&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-791.697C342.213,-783.983 341.551,-774.712 340.937,-766.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-765.83 340.222,-756.104 337.443,-766.328 344.425,-765.83"/>
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<!-- 26 -->
<g id="node27" class="node"><title>26</title>
<path fill="none" stroke="#56d89a" stroke-width="2" d="M238.5,-828C238.5,-828 151.5,-828 151.5,-828 145.5,-828 139.5,-822 139.5,-816 139.5,-816 139.5,-804 139.5,-804 139.5,-798 145.5,-792 151.5,-792 151.5,-792 238.5,-792 238.5,-792 244.5,-792 250.5,-798 250.5,-804 250.5,-804 250.5,-816 250.5,-816 250.5,-822 244.5,-828 238.5,-828"/>
<text text-anchor="middle" x="195" y="-807.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 26&#45;&gt;15 -->
<g id="edge30" class="edge"><title>26&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M195,-791.697C195,-783.983 195,-774.712 195,-766.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-766.104 195,-756.104 191.5,-766.104 198.5,-766.104"/>
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<!-- 29 -->
<g id="node30" class="node"><title>29</title>
<path fill="none" stroke="#88d856" stroke-width="2" d="M522.5,-756C522.5,-756 437.5,-756 437.5,-756 431.5,-756 425.5,-750 425.5,-744 425.5,-744 425.5,-732 425.5,-732 425.5,-726 431.5,-720 437.5,-720 437.5,-720 522.5,-720 522.5,-720 528.5,-720 534.5,-726 534.5,-732 534.5,-732 534.5,-744 534.5,-744 534.5,-750 528.5,-756 522.5,-756"/>
<text text-anchor="middle" x="480" y="-735.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 26&#45;&gt;29 -->
<g id="edge49" class="edge"><title>26&#45;&gt;29</title>
<path fill="none" stroke="grey" stroke-width="2" d="M250.642,-794.334C253.806,-793.536 256.942,-792.753 260,-792 326.125,-775.727 345.31,-773.324 415.453,-756.091"/>
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<!-- 27 -->
<g id="node28" class="node"><title>27</title>
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<text text-anchor="middle" x="613" y="-807.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 27&#45;&gt;16 -->
<g id="edge31" class="edge"><title>27&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M613,-791.697C613,-783.983 613,-774.712 613,-766.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-766.104 613,-756.104 609.5,-766.104 616.5,-766.104"/>
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<!-- 28&#45;&gt;17 -->
<g id="edge32" class="edge"><title>28&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M688.06,-503.966C660.535,-494.185 625.783,-481.836 596.759,-471.524"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-468.161 587.155,-468.111 595.406,-474.757 597.749,-468.161"/>
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<!-- 29&#45;&gt;18 -->
<g id="edge33" class="edge"><title>29&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-719.697C456.43,-711.22 446.961,-700.864 438.476,-691.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-689.123 431.638,-684.104 435.803,-693.846 440.969,-689.123"/>
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<!-- 29&#45;&gt;19 -->
<g id="edge35" class="edge"><title>29&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-719.697C507.062,-711.05 518.118,-700.449 527.943,-691.027"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-693.552 535.163,-684.104 525.522,-688.499 530.367,-693.552"/>
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<!-- 30 -->
<g id="node31" class="node"><title>30</title>
<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1001,-756C1001,-756 931,-756 931,-756 925,-756 919,-750 919,-744 919,-744 919,-732 919,-732 919,-726 925,-720 931,-720 931,-720 1001,-720 1001,-720 1007,-720 1013,-726 1013,-732 1013,-732 1013,-744 1013,-744 1013,-750 1007,-756 1001,-756"/>
<text text-anchor="middle" x="966" y="-735.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 30&#45;&gt;20 -->
<g id="edge37" class="edge"><title>30&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-719.876C919.68,-710.639 899.458,-699.131 882.029,-689.212"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="883.627,-686.094 873.205,-684.19 880.165,-692.178 883.627,-686.094"/>
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<!-- 30&#45;&gt;22 -->
<g id="edge41" class="edge"><title>30&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M966,-719.697C966,-711.983 966,-702.712 966,-694.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-694.104 966,-684.104 962.5,-694.104 969.5,-694.104"/>
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<!-- 30&#45;&gt;24 -->
<g id="edge44" class="edge"><title>30&#45;&gt;24</title>
<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-719.775C1005.11,-710.718 1017.62,-698.478 1024,-684 1043.27,-640.297 1032.42,-583.371 1023.04,-550.235"/>
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<!-- 31 -->
<g id="node32" class="node"><title>31</title>
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<!-- 31&#45;&gt;28 -->
<g id="edge47" class="edge"><title>31&#45;&gt;28</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-548.763 711.198,-540.19 700.985,-543.009 704.972,-548.763"/>
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