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="472" 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="72" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge12" 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="147" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 5&#45;&gt;3 -->
<g id="edge9" 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="652" y="-735.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 6&#45;&gt;3 -->
<g id="edge4" 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="edge7" 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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<!-- 8&#45;&gt;3 -->
<g id="edge10" 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="472" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
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<!-- 9&#45;&gt;3 -->
<g id="edge6" 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="308" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
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<!-- 10&#45;&gt;3 -->
<g id="edge5" 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="927" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 11&#45;&gt;3 -->
<g id="edge8" class="edge"><title>11&#45;&gt;3</title>
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<!-- 33 -->
<g id="node34" class="node"><title>33</title>
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<text text-anchor="middle" x="927" y="-519.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<!-- 11&#45;&gt;33 -->
<g id="edge50" class="edge"><title>11&#45;&gt;33</title>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="887" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
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<!-- 12&#45;&gt;3 -->
<g id="edge11" 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="688" y="-807.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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<!-- 13&#45;&gt;6 -->
<g id="edge13" class="edge"><title>13&#45;&gt;6</title>
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<!-- 17 -->
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<text text-anchor="middle" x="462" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 13&#45;&gt;17 -->
<g id="edge30" class="edge"><title>13&#45;&gt;17</title>
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<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<text text-anchor="middle" x="995" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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<!-- 13&#45;&gt;19 -->
<g id="edge34" class="edge"><title>13&#45;&gt;19</title>
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<!-- 14 -->
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<text text-anchor="middle" x="406" y="-807.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
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<!-- 14&#45;&gt;6 -->
<g id="edge14" class="edge"><title>14&#45;&gt;6</title>
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<!-- 14&#45;&gt;7 -->
<g id="edge16" class="edge"><title>14&#45;&gt;7</title>
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<!-- 15 -->
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<!-- 15&#45;&gt;7 -->
<g id="edge15" class="edge"><title>15&#45;&gt;7</title>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
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<!-- 15&#45;&gt;18 -->
<g id="edge32" class="edge"><title>15&#45;&gt;18</title>
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<!-- 21 -->
<g id="node22" class="node"><title>21</title>
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<!-- 15&#45;&gt;21 -->
<g id="edge38" class="edge"><title>15&#45;&gt;21</title>
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<!-- 16 -->
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<!-- 16&#45;&gt;8 -->
<g id="edge17" class="edge"><title>16&#45;&gt;8</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="660.838,-405.501 655.784,-396.189 653.928,-406.62 660.838,-405.501"/>
</g>
<!-- 17&#45;&gt;9 -->
<g id="edge18" class="edge"><title>17&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M464.472,-647.697C465.574,-639.983 466.898,-630.712 468.127,-622.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="471.607,-622.499 469.557,-612.104 464.677,-621.509 471.607,-622.499"/>
</g>
<!-- 17&#45;&gt;10 -->
<g id="edge20" class="edge"><title>17&#45;&gt;10</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="356.102,-613.02 345.55,-612.068 353.206,-619.393 356.102,-613.02"/>
</g>
<!-- 18&#45;&gt;9 -->
<g id="edge19" class="edge"><title>18&#45;&gt;9</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="425.228,-619.283 432.987,-612.068 422.422,-612.87 425.228,-619.283"/>
</g>
<!-- 18&#45;&gt;10 -->
<g id="edge21" class="edge"><title>18&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M311.011,-647.697C310.57,-639.983 310.041,-630.712 309.549,-622.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="313.042,-621.888 308.977,-612.104 306.054,-622.288 313.042,-621.888"/>
</g>
<!-- 19&#45;&gt;11 -->
<g id="edge24" class="edge"><title>19&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M998.427,-719.921C1001.3,-701.221 1003.33,-670.855 992,-648 985.547,-634.983 974.25,-624.061 962.865,-615.579"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="964.832,-612.685 954.627,-609.839 960.83,-618.428 964.832,-612.685"/>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
<path fill="none" stroke="#56d8b9" stroke-width="2" d="M955,-684C955,-684 805,-684 805,-684 799,-684 793,-678 793,-672 793,-672 793,-660 793,-660 793,-654 799,-648 805,-648 805,-648 955,-648 955,-648 961,-648 967,-654 967,-660 967,-660 967,-672 967,-672 967,-678 961,-684 955,-684"/>
<text text-anchor="middle" x="880" y="-663.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 19&#45;&gt;20 -->
<g id="edge37" class="edge"><title>19&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M966.868,-719.876C951.832,-710.724 933.133,-699.342 916.94,-689.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="918.602,-686.4 908.24,-684.19 914.962,-692.379 918.602,-686.4"/>
</g>
<!-- 26 -->
<g id="node27" class="node"><title>26</title>
<path fill="none" stroke="#56d86b" stroke-width="2" d="M746,-612C746,-612 658,-612 658,-612 652,-612 646,-606 646,-600 646,-600 646,-588 646,-588 646,-582 652,-576 658,-576 658,-576 746,-576 746,-576 752,-576 758,-582 758,-588 758,-588 758,-600 758,-600 758,-606 752,-612 746,-612"/>
<text text-anchor="middle" x="702" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 19&#45;&gt;26 -->
<g id="edge44" class="edge"><title>19&#45;&gt;26</title>
<path fill="none" stroke="grey" stroke-width="2" d="M996.5,-719.984C997.261,-699.884 995.174,-666.809 976,-648 947.195,-619.744 839.886,-605.821 768.42,-599.541"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="768.409,-596.027 758.149,-598.669 767.817,-603.002 768.409,-596.027"/>
</g>
<!-- 20&#45;&gt;11 -->
<g id="edge23" class="edge"><title>20&#45;&gt;11</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="912.847,-622.358 915.516,-612.104 907.035,-618.456 912.847,-622.358"/>
</g>
<!-- 20&#45;&gt;26 -->
<g id="edge43" class="edge"><title>20&#45;&gt;26</title>
<path fill="none" stroke="grey" stroke-width="2" d="M836.456,-647.876C811.798,-638.179 780.777,-625.98 754.746,-615.743"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="755.989,-612.471 745.402,-612.068 753.428,-618.985 755.989,-612.471"/>
</g>
<!-- 21&#45;&gt;11 -->
<g id="edge22" class="edge"><title>21&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M916.362,-719.889C941.372,-709.243 968.986,-695.447 976,-684 984.359,-670.357 981.832,-662.899 976,-648 971.803,-637.279 964.308,-627.427 956.422,-619.201"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="958.76,-616.592 949.153,-612.125 953.877,-621.608 958.76,-616.592"/>
</g>
<!-- 21&#45;&gt;20 -->
<g id="edge36" class="edge"><title>21&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M873.978,-719.697C874.859,-711.983 875.919,-702.712 876.901,-694.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="880.387,-694.437 878.045,-684.104 873.432,-693.642 880.387,-694.437"/>
</g>
<!-- 21&#45;&gt;26 -->
<g id="edge41" class="edge"><title>21&#45;&gt;26</title>
<path fill="none" stroke="grey" stroke-width="2" d="M823.356,-730.106C753.776,-719.753 632.766,-699.73 620,-684 609.918,-671.576 612.35,-662.053 620,-648 626.913,-635.301 638.322,-625.181 650.465,-617.33"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="652.587,-620.14 659.382,-612.011 649.001,-614.128 652.587,-620.14"/>
</g>
<!-- 22 -->
<g id="node23" class="node"><title>22</title>
<path fill="none" stroke="#5682d8" stroke-width="2" d="M941.5,-396C941.5,-396 860.5,-396 860.5,-396 854.5,-396 848.5,-390 848.5,-384 848.5,-384 848.5,-372 848.5,-372 848.5,-366 854.5,-360 860.5,-360 860.5,-360 941.5,-360 941.5,-360 947.5,-360 953.5,-366 953.5,-372 953.5,-372 953.5,-384 953.5,-384 953.5,-390 947.5,-396 941.5,-396"/>
<text text-anchor="middle" x="901" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 22&#45;&gt;12 -->
<g id="edge25" class="edge"><title>22&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M897.539,-359.697C895.997,-351.983 894.142,-342.712 892.422,-334.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="895.814,-333.224 890.421,-324.104 888.95,-334.597 895.814,-333.224"/>
</g>
<!-- 23 -->
<g id="node24" class="node"><title>23</title>
<path fill="none" stroke="#61d856" stroke-width="2" d="M758,-900C758,-900 632,-900 632,-900 626,-900 620,-894 620,-888 620,-888 620,-876 620,-876 620,-870 626,-864 632,-864 632,-864 758,-864 758,-864 764,-864 770,-870 770,-876 770,-876 770,-888 770,-888 770,-894 764,-900 758,-900"/>
<text text-anchor="middle" x="695" y="-879.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 23&#45;&gt;13 -->
<g id="edge26" class="edge"><title>23&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M693.27,-863.697C692.498,-855.983 691.571,-846.712 690.711,-838.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="694.188,-837.706 689.71,-828.104 687.223,-838.403 694.188,-837.706"/>
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<!-- 24 -->
<g id="node25" class="node"><title>24</title>
<path fill="none" stroke="#d89556" stroke-width="2" d="M359.5,-900C359.5,-900 272.5,-900 272.5,-900 266.5,-900 260.5,-894 260.5,-888 260.5,-888 260.5,-876 260.5,-876 260.5,-870 266.5,-864 272.5,-864 272.5,-864 359.5,-864 359.5,-864 365.5,-864 371.5,-870 371.5,-876 371.5,-876 371.5,-888 371.5,-888 371.5,-894 365.5,-900 359.5,-900"/>
<text text-anchor="middle" x="316" y="-879.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 24&#45;&gt;14 -->
<g id="edge27" class="edge"><title>24&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M338.247,-863.697C349.582,-854.881 363.53,-844.032 375.819,-834.474"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="378.264,-837.007 384.009,-828.104 373.966,-831.481 378.264,-837.007"/>
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<!-- 31 -->
<g id="node32" class="node"><title>31</title>
<path fill="none" stroke="#d86656" stroke-width="2" d="M321.5,-828C321.5,-828 150.5,-828 150.5,-828 144.5,-828 138.5,-822 138.5,-816 138.5,-816 138.5,-804 138.5,-804 138.5,-798 144.5,-792 150.5,-792 150.5,-792 321.5,-792 321.5,-792 327.5,-792 333.5,-798 333.5,-804 333.5,-804 333.5,-816 333.5,-816 333.5,-822 327.5,-828 321.5,-828"/>
<text text-anchor="middle" x="236" y="-807.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
</g>
<!-- 24&#45;&gt;31 -->
<g id="edge49" class="edge"><title>24&#45;&gt;31</title>
<path fill="none" stroke="grey" stroke-width="2" d="M296.225,-863.697C286.246,-854.965 273.989,-844.24 263.143,-834.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="265.378,-832.055 255.548,-828.104 260.769,-837.323 265.378,-832.055"/>
</g>
<!-- 25 -->
<g id="node26" class="node"><title>25</title>
<path fill="none" stroke="#c6d856" stroke-width="2" d="M590,-900C590,-900 480,-900 480,-900 474,-900 468,-894 468,-888 468,-888 468,-876 468,-876 468,-870 474,-864 480,-864 480,-864 590,-864 590,-864 596,-864 602,-870 602,-876 602,-876 602,-888 602,-888 602,-894 596,-900 590,-900"/>
<text text-anchor="middle" x="535" y="-879.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 25&#45;&gt;15 -->
<g id="edge28" class="edge"><title>25&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M535.742,-863.697C536.072,-855.983 536.469,-846.712 536.838,-838.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="540.335,-838.245 537.267,-828.104 533.342,-837.945 540.335,-838.245"/>
</g>
<!-- 26&#45;&gt;16 -->
<g id="edge29" class="edge"><title>26&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M695.573,-575.697C692.645,-567.813 689.113,-558.304 685.86,-549.546"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="689.116,-548.26 682.353,-540.104 682.554,-550.697 689.116,-548.26"/>
</g>
<!-- 27 -->
<g id="node28" class="node"><title>27</title>
<path fill="none" stroke="#d85656" stroke-width="2" d="M283.5,-756C283.5,-756 198.5,-756 198.5,-756 192.5,-756 186.5,-750 186.5,-744 186.5,-744 186.5,-732 186.5,-732 186.5,-726 192.5,-720 198.5,-720 198.5,-720 283.5,-720 283.5,-720 289.5,-720 295.5,-726 295.5,-732 295.5,-732 295.5,-744 295.5,-744 295.5,-750 289.5,-756 283.5,-756"/>
<text text-anchor="middle" x="241" y="-735.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 27&#45;&gt;17 -->
<g id="edge31" class="edge"><title>27&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M294.78,-719.966C325.927,-710.1 365.323,-697.622 398.052,-687.255"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="399.502,-690.467 407.979,-684.111 397.389,-683.794 399.502,-690.467"/>
</g>
<!-- 27&#45;&gt;18 -->
<g id="edge33" class="edge"><title>27&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M258.551,-719.697C267.234,-711.135 277.863,-700.656 287.348,-691.304"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="289.988,-693.617 294.651,-684.104 285.073,-688.633 289.988,-693.617"/>
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<!-- 28 -->
<g id="node29" class="node"><title>28</title>
<path fill="none" stroke="#5663d8" stroke-width="2" d="M1030,-828C1030,-828 960,-828 960,-828 954,-828 948,-822 948,-816 948,-816 948,-804 948,-804 948,-798 954,-792 960,-792 960,-792 1030,-792 1030,-792 1036,-792 1042,-798 1042,-804 1042,-804 1042,-816 1042,-816 1042,-822 1036,-828 1030,-828"/>
<text text-anchor="middle" x="995" y="-807.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 28&#45;&gt;19 -->
<g id="edge35" class="edge"><title>28&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M995,-791.697C995,-783.983 995,-774.712 995,-766.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="998.5,-766.104 995,-756.104 991.5,-766.104 998.5,-766.104"/>
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<!-- 28&#45;&gt;21 -->
<g id="edge39" class="edge"><title>28&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M964.911,-791.876C948.68,-782.639 928.458,-771.131 911.029,-761.212"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="912.627,-758.094 902.205,-756.19 909.165,-764.178 912.627,-758.094"/>
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<!-- 34 -->
<g id="node35" class="node"><title>34</title>
<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1126,-540C1126,-540 1046,-540 1046,-540 1040,-540 1034,-534 1034,-528 1034,-528 1034,-516 1034,-516 1034,-510 1040,-504 1046,-504 1046,-504 1126,-504 1126,-504 1132,-504 1138,-510 1138,-516 1138,-516 1138,-528 1138,-528 1138,-534 1132,-540 1126,-540"/>
<text text-anchor="middle" x="1086" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
<!-- 28&#45;&gt;34 -->
<g id="edge51" class="edge"><title>28&#45;&gt;34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1025.63,-791.97C1038.75,-783.028 1052.89,-770.827 1061,-756 1097.51,-689.252 1094.02,-595.687 1089.49,-550.104"/>
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<!-- 29 -->
<g id="node30" class="node"><title>29</title>
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<text text-anchor="middle" x="927" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 29&#45;&gt;22 -->
<g id="edge40" class="edge"><title>29&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M920.573,-431.697C917.645,-423.813 914.113,-414.304 910.86,-405.546"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="914.116,-404.26 907.353,-396.104 907.554,-406.697 914.116,-404.26"/>
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<!-- 30 -->
<g id="node31" class="node"><title>30</title>
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<text text-anchor="middle" x="702" y="-663.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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<!-- 30&#45;&gt;26 -->
<g id="edge42" class="edge"><title>30&#45;&gt;26</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="705.5,-622.104 702,-612.104 698.5,-622.104 705.5,-622.104"/>
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<!-- 31&#45;&gt;27 -->
<g id="edge45" class="edge"><title>31&#45;&gt;27</title>
<path fill="none" stroke="grey" stroke-width="2" d="M237.236,-791.697C237.787,-783.983 238.449,-774.712 239.063,-766.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="242.557,-766.328 239.778,-756.104 235.575,-765.83 242.557,-766.328"/>
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<!-- 32 -->
<g id="node33" class="node"><title>32</title>
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<text text-anchor="middle" x="60" y="-807.5" font-family="sans" font-size="10.00">extract_decoys_salmon</text>
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<!-- 32&#45;&gt;27 -->
<g id="edge46" class="edge"><title>32&#45;&gt;27</title>
<path fill="none" stroke="grey" stroke-width="2" d="M104.278,-791.876C129.351,-782.179 160.896,-769.98 187.365,-759.743"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="188.802,-762.94 196.866,-756.068 186.277,-756.411 188.802,-762.94"/>
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<!-- 33&#45;&gt;29 -->
<g id="edge47" class="edge"><title>33&#45;&gt;29</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="930.5,-478.104 927,-468.104 923.5,-478.104 930.5,-478.104"/>
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<!-- 34&#45;&gt;29 -->
<g id="edge48" class="edge"><title>34&#45;&gt;29</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1047.1,-503.876C1021.51,-492.607 988.231,-477.957 963.198,-466.936"/>
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