diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 0234a267d8a2d2e77fde6135d2b7b08cf17cbf35..057f53177f975bc351b03b7bee1dc2f4af1e51fa 100644
--- a/images/rule_graph.svg
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@@ -4,598 +4,598 @@
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+<title>14</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M784.0684,-540C784.0684,-540 691.9316,-540 691.9316,-540 685.9316,-540 679.9316,-534 679.9316,-528 679.9316,-528 679.9316,-516 679.9316,-516 679.9316,-510 685.9316,-504 691.9316,-504 691.9316,-504 784.0684,-504 784.0684,-504 790.0684,-504 796.0684,-510 796.0684,-516 796.0684,-516 796.0684,-528 796.0684,-528 796.0684,-534 790.0684,-540 784.0684,-540"/>
+<text text-anchor="middle" x="738" y="-519" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 5->13 -->
-<g id="edge29" class="edge">
-<title>5->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M607.0093,-510.2297C668.3055,-499.746 759.7105,-483.681 839,-468 843.7236,-467.0658 848.5926,-466.0771 853.4932,-465.0629"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="854.4898,-468.4302 863.5601,-462.9547 853.055,-461.5788 854.4898,-468.4302"/>
+<!-- 5->14 -->
+<g id="edge31" class="edge">
+<title>5->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M308.7185,-579.1041C314.5546,-578.0007 320.3727,-576.9496 326,-576 446.4017,-555.6826 587.6969,-538.6257 669.6233,-529.3996"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="670.255,-532.8508 679.8031,-528.2591 669.4756,-525.8943 670.255,-532.8508"/>
</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M650.9137,-324C650.9137,-324 545.0863,-324 545.0863,-324 539.0863,-324 533.0863,-318 533.0863,-312 533.0863,-312 533.0863,-300 533.0863,-300 533.0863,-294 539.0863,-288 545.0863,-288 545.0863,-288 650.9137,-288 650.9137,-288 656.9137,-288 662.9137,-294 662.9137,-300 662.9137,-300 662.9137,-312 662.9137,-312 662.9137,-318 656.9137,-324 650.9137,-324"/>
-<text text-anchor="middle" x="598" y="-303" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M509.9137,-324C509.9137,-324 404.0863,-324 404.0863,-324 398.0863,-324 392.0863,-318 392.0863,-312 392.0863,-312 392.0863,-300 392.0863,-300 392.0863,-294 398.0863,-288 404.0863,-288 404.0863,-288 509.9137,-288 509.9137,-288 515.9137,-288 521.9137,-294 521.9137,-300 521.9137,-300 521.9137,-312 521.9137,-312 521.9137,-318 515.9137,-324 509.9137,-324"/>
+<text text-anchor="middle" x="457" y="-303" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
</g>
-<!-- 5->24 -->
+<!-- 5->25 -->
<g id="edge46" class="edge">
-<title>5->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M536.2262,-503.7367C535.5703,-472.9041 537.0431,-409.0916 557,-360 560.9896,-350.186 567.2415,-340.5983 573.6719,-332.2907"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="576.4635,-334.4058 580.0845,-324.4489 571.0447,-329.9745 576.4635,-334.4058"/>
+<title>5->25</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M248.1958,-575.9744C269.6593,-534.9039 326.1863,-432.3411 391,-360 400.5257,-349.368 412.2388,-339.0844 423.1401,-330.395"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="425.5178,-332.98 431.2685,-324.0816 421.2239,-327.4516 425.5178,-332.98"/>
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<!-- 6->5 -->
<g id="edge18" class="edge">
<title>6->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M535.5047,-575.8314C535.7186,-568.131 535.9729,-558.9743 536.2106,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="539.7094,-550.5066 536.4885,-540.4133 532.7121,-550.3122 539.7094,-550.5066"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M233.7664,-647.8314C234.515,-640.131 235.4053,-630.9743 236.2373,-622.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="239.7256,-622.7051 237.2098,-612.4133 232.7585,-622.0276 239.7256,-622.7051"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M291.8894,-396C291.8894,-396 206.1106,-396 206.1106,-396 200.1106,-396 194.1106,-390 194.1106,-384 194.1106,-384 194.1106,-372 194.1106,-372 194.1106,-366 200.1106,-360 206.1106,-360 206.1106,-360 291.8894,-360 291.8894,-360 297.8894,-360 303.8894,-366 303.8894,-372 303.8894,-372 303.8894,-384 303.8894,-384 303.8894,-390 297.8894,-396 291.8894,-396"/>
-<text text-anchor="middle" x="249" y="-375" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M241.8894,-396C241.8894,-396 156.1106,-396 156.1106,-396 150.1106,-396 144.1106,-390 144.1106,-384 144.1106,-384 144.1106,-372 144.1106,-372 144.1106,-366 150.1106,-360 156.1106,-360 156.1106,-360 241.8894,-360 241.8894,-360 247.8894,-360 253.8894,-366 253.8894,-372 253.8894,-372 253.8894,-384 253.8894,-384 253.8894,-390 247.8894,-396 241.8894,-396"/>
+<text text-anchor="middle" x="199" y="-375" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
<!-- 7->4 -->
-<g id="edge17" class="edge">
+<g id="edge16" class="edge">
<title>7->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M261.8695,-359.8314C267.6835,-351.6232 274.6696,-341.7606 281.0646,-332.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="284.0331,-334.5966 286.9573,-324.4133 278.321,-330.5505 284.0331,-334.5966"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M177.8033,-359.8314C167.5566,-351.0485 155.0997,-340.3712 143.9903,-330.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="146.0603,-328.0134 136.19,-324.1628 141.5048,-333.3282 146.0603,-328.0134"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M185.258,-324C185.258,-324 56.742,-324 56.742,-324 50.742,-324 44.742,-318 44.742,-312 44.742,-312 44.742,-300 44.742,-300 44.742,-294 50.742,-288 56.742,-288 56.742,-288 185.258,-288 185.258,-288 191.258,-288 197.258,-294 197.258,-300 197.258,-300 197.258,-312 197.258,-312 197.258,-318 191.258,-324 185.258,-324"/>
-<text text-anchor="middle" x="121" y="-303" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M358.258,-324C358.258,-324 229.742,-324 229.742,-324 223.742,-324 217.742,-318 217.742,-312 217.742,-312 217.742,-300 217.742,-300 217.742,-294 223.742,-288 229.742,-288 229.742,-288 358.258,-288 358.258,-288 364.258,-288 370.258,-294 370.258,-300 370.258,-300 370.258,-312 370.258,-312 370.258,-318 364.258,-324 358.258,-324"/>
+<text text-anchor="middle" x="294" y="-303" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
</g>
<!-- 7->9 -->
-<g id="edge21" class="edge">
+<g id="edge22" class="edge">
<title>7->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M216.7002,-359.8314C200.1766,-350.5368 179.8814,-339.1208 162.2393,-329.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="163.7212,-326.015 153.2895,-324.1628 160.2893,-332.116 163.7212,-326.015"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M222.9725,-359.8314C234.7861,-350.8779 249.1972,-339.9558 261.9435,-330.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="264.1795,-332.9925 270.0352,-324.1628 259.9514,-327.4137 264.1795,-332.9925"/>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M169.1476,-540C169.1476,-540 80.8524,-540 80.8524,-540 74.8524,-540 68.8524,-534 68.8524,-528 68.8524,-528 68.8524,-516 68.8524,-516 68.8524,-510 74.8524,-504 80.8524,-504 80.8524,-504 169.1476,-504 169.1476,-504 175.1476,-504 181.1476,-510 181.1476,-516 181.1476,-516 181.1476,-528 181.1476,-528 181.1476,-534 175.1476,-540 169.1476,-540"/>
-<text text-anchor="middle" x="125" y="-519" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M546.1476,-540C546.1476,-540 457.8524,-540 457.8524,-540 451.8524,-540 445.8524,-534 445.8524,-528 445.8524,-528 445.8524,-516 445.8524,-516 445.8524,-510 451.8524,-504 457.8524,-504 457.8524,-504 546.1476,-504 546.1476,-504 552.1476,-504 558.1476,-510 558.1476,-516 558.1476,-516 558.1476,-528 558.1476,-528 558.1476,-534 552.1476,-540 546.1476,-540"/>
+<text text-anchor="middle" x="502" y="-519" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
</g>
<!-- 8->7 -->
<g id="edge20" class="edge">
<title>8->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M90.911,-503.9135C77.7792,-495.0032 64.2103,-482.9331 57,-468 50.0431,-453.5916 47.3385,-444.7536 57,-432 72.5024,-411.5361 134.4643,-396.6613 183.8625,-387.7667"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="184.6275,-391.1861 193.8739,-386.0136 183.4201,-384.291 184.6275,-391.1861"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M463.9316,-503.9081C408.7121,-477.6652 306.4502,-429.0655 246.4107,-400.5318"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="247.6852,-397.2624 237.151,-396.1311 244.6805,-403.5848 247.6852,-397.2624"/>
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-<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M254.0708,-468C254.0708,-468 77.9292,-468 77.9292,-468 71.9292,-468 65.9292,-462 65.9292,-456 65.9292,-456 65.9292,-444 65.9292,-444 65.9292,-438 71.9292,-432 77.9292,-432 77.9292,-432 254.0708,-432 254.0708,-432 260.0708,-432 266.0708,-438 266.0708,-444 266.0708,-444 266.0708,-456 266.0708,-456 266.0708,-462 260.0708,-468 254.0708,-468"/>
-<text text-anchor="middle" x="166" y="-447" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
+<!-- 27 -->
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M612.0708,-468C612.0708,-468 435.9292,-468 435.9292,-468 429.9292,-468 423.9292,-462 423.9292,-456 423.9292,-456 423.9292,-444 423.9292,-444 423.9292,-438 429.9292,-432 435.9292,-432 435.9292,-432 612.0708,-432 612.0708,-432 618.0708,-432 624.0708,-438 624.0708,-444 624.0708,-444 624.0708,-456 624.0708,-456 624.0708,-462 618.0708,-468 612.0708,-468"/>
+<text text-anchor="middle" x="524" y="-447" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
</g>
-<!-- 8->26 -->
-<g id="edge50" class="edge">
-<title>8->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M135.346,-503.8314C139.9237,-495.7925 145.4052,-486.1666 150.4588,-477.2918"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="153.6077,-478.8351 155.5147,-468.4133 147.5248,-475.3712 153.6077,-478.8351"/>
+<!-- 8->27 -->
+<g id="edge49" class="edge">
+<title>8->27</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M507.5515,-503.8314C509.9303,-496.0463 512.7638,-486.7729 515.4033,-478.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="518.7987,-478.9996 518.3737,-468.4133 512.1042,-476.954 518.7987,-478.9996"/>
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<!-- 9->1 -->
<g id="edge8" class="edge">
<title>9->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M94.2769,-287.9104C82.9915,-278.6439 71.074,-266.295 65,-252 58.743,-237.2742 56.1221,-229.311 65,-216 100.676,-162.5099 288.1289,-118.2864 379.219,-99.5881"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="379.9401,-103.0132 389.0439,-97.5937 378.5474,-96.1531 379.9401,-103.0132"/>
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-<!-- 9->30 -->
-<g id="edge58" class="edge">
-<title>9->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M161.3748,-287.8314C182.6787,-278.2446 208.9983,-266.4008 231.5211,-256.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="233.2326,-259.3334 240.9156,-252.038 230.3601,-252.95 233.2326,-259.3334"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M312.0371,-287.744C321.0825,-277.8168 331.6472,-264.9459 339,-252 364.1302,-207.754 347.3293,-185.3387 377,-144 385.1284,-132.6752 396.2792,-122.5385 407.2469,-114.1906"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="409.5096,-116.873 415.5453,-108.1655 405.3969,-111.2086 409.5096,-116.873"/>
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<!-- 9->31 -->
-<g id="edge60" class="edge">
+<g id="edge57" class="edge">
<title>9->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M125.7945,-287.8314C127.8489,-280.0463 130.296,-270.7729 132.5756,-262.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="135.9735,-262.9753 135.1409,-252.4133 129.2052,-261.1892 135.9735,-262.9753"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M288.7008,-287.8314C286.4302,-280.0463 283.7254,-270.7729 281.206,-262.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="284.5306,-261.0332 278.3705,-252.4133 277.8106,-262.9933 284.5306,-261.0332"/>
+</g>
+<!-- 9->32 -->
+<g id="edge59" class="edge">
+<title>9->32</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M253.1206,-287.8314C231.454,-278.2018 204.6637,-266.295 181.7922,-256.1299"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="183.1451,-252.9011 172.5855,-252.038 180.3021,-259.2978 183.1451,-252.9011"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
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-<text text-anchor="middle" x="370" y="-519" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M445.2386,-612C445.2386,-612 346.7614,-612 346.7614,-612 340.7614,-612 334.7614,-606 334.7614,-600 334.7614,-600 334.7614,-588 334.7614,-588 334.7614,-582 340.7614,-576 346.7614,-576 346.7614,-576 445.2386,-576 445.2386,-576 451.2386,-576 457.2386,-582 457.2386,-588 457.2386,-588 457.2386,-600 457.2386,-600 457.2386,-606 451.2386,-612 445.2386,-612"/>
+<text text-anchor="middle" x="396" y="-591" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
<!-- 10->9 -->
-<g id="edge22" class="edge">
+<g id="edge21" class="edge">
<title>10->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M354.8082,-503.9899C337.2779,-484.1397 306.7627,-452.3339 275,-432 238.7168,-408.7722 218.8594,-422.6372 185,-396 163.4058,-379.0118 145.9329,-352.8408 134.7339,-333.0912"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="137.7669,-331.3428 129.8937,-324.253 131.6273,-334.7051 137.7669,-331.3428"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M385.5394,-575.8623C366.4169,-541.818 325.9546,-465.5016 306,-396 300.209,-375.83 297.1958,-352.2998 295.6374,-334.3584"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="299.1166,-333.9519 294.8606,-324.2495 292.1372,-334.4883 299.1166,-333.9519"/>
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-<g id="node18" class="node">
-<title>17</title>
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-<text text-anchor="middle" x="780" y="-447" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<!-- 18 -->
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M901.8845,-540C901.8845,-540 826.1155,-540 826.1155,-540 820.1155,-540 814.1155,-534 814.1155,-528 814.1155,-528 814.1155,-516 814.1155,-516 814.1155,-510 820.1155,-504 826.1155,-504 826.1155,-504 901.8845,-504 901.8845,-504 907.8845,-504 913.8845,-510 913.8845,-516 913.8845,-516 913.8845,-528 913.8845,-528 913.8845,-534 907.8845,-540 901.8845,-540"/>
+<text text-anchor="middle" x="864" y="-519" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
</g>
-<!-- 10->17 -->
-<g id="edge34" class="edge">
-<title>10->17</title>
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+<!-- 10->18 -->
+<g id="edge33" class="edge">
+<title>10->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M457.5206,-589.063C535.9865,-582.0602 675.8796,-567.2082 804.2506,-539.9607"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="805.2196,-543.3324 814.2589,-537.8058 803.7462,-536.4892 805.2196,-543.3324"/>
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-<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M503.2288,-324C503.2288,-324 414.7712,-324 414.7712,-324 408.7712,-324 402.7712,-318 402.7712,-312 402.7712,-312 402.7712,-300 402.7712,-300 402.7712,-294 408.7712,-288 414.7712,-288 414.7712,-288 503.2288,-288 503.2288,-288 509.2288,-288 515.2288,-294 515.2288,-300 515.2288,-300 515.2288,-312 515.2288,-312 515.2288,-318 509.2288,-324 503.2288,-324"/>
-<text text-anchor="middle" x="459" y="-303" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<!-- 28 -->
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M640.2288,-324C640.2288,-324 551.7712,-324 551.7712,-324 545.7712,-324 539.7712,-318 539.7712,-312 539.7712,-312 539.7712,-300 539.7712,-300 539.7712,-294 545.7712,-288 551.7712,-288 551.7712,-288 640.2288,-288 640.2288,-288 646.2288,-288 652.2288,-294 652.2288,-300 652.2288,-300 652.2288,-312 652.2288,-312 652.2288,-318 646.2288,-324 640.2288,-324"/>
+<text text-anchor="middle" x="596" y="-303" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
</g>
-<!-- 10->27 -->
-<g id="edge52" class="edge">
-<title>10->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M367.757,-503.5876C364.8173,-471.9783 362.7678,-406.3259 389,-360 395.6896,-348.1862 406.1133,-338.0894 416.8921,-329.9336"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="419.0155,-332.7185 425.1479,-324.0788 414.9662,-327.0086 419.0155,-332.7185"/>
+<!-- 10->28 -->
+<g id="edge50" class="edge">
+<title>10->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M391.261,-575.6963C381.3043,-532.6807 363.1697,-423.9709 415,-360 416.9394,-357.6064 479.0019,-339.4069 529.9154,-324.7878"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="530.9531,-328.1314 539.6014,-322.011 529.024,-321.4024 530.9531,-328.1314"/>
</g>
<!-- 11->10 -->
<g id="edge23" class="edge">
<title>11->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M370,-575.8314C370,-568.131 370,-558.9743 370,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="373.5001,-550.4132 370,-540.4133 366.5001,-550.4133 373.5001,-550.4132"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M396,-647.8314C396,-640.131 396,-630.9743 396,-622.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="399.5001,-622.4132 396,-612.4133 392.5001,-622.4133 399.5001,-622.4132"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M786.1524,-324C786.1524,-324 697.8476,-324 697.8476,-324 691.8476,-324 685.8476,-318 685.8476,-312 685.8476,-312 685.8476,-300 685.8476,-300 685.8476,-294 691.8476,-288 697.8476,-288 697.8476,-288 786.1524,-288 786.1524,-288 792.1524,-288 798.1524,-294 798.1524,-300 798.1524,-300 798.1524,-312 798.1524,-312 798.1524,-318 792.1524,-324 786.1524,-324"/>
-<text text-anchor="middle" x="742" y="-303" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<path fill="none" stroke="#56b9d8" stroke-width="2" d="M774.1524,-324C774.1524,-324 685.8476,-324 685.8476,-324 679.8476,-324 673.8476,-318 673.8476,-312 673.8476,-312 673.8476,-300 673.8476,-300 673.8476,-294 679.8476,-288 685.8476,-288 685.8476,-288 774.1524,-288 774.1524,-288 780.1524,-288 786.1524,-294 786.1524,-300 786.1524,-300 786.1524,-312 786.1524,-312 786.1524,-318 780.1524,-324 774.1524,-324"/>
+<text text-anchor="middle" x="730" y="-303" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 12->1 -->
-<g id="edge13" class="edge">
+<g id="edge9" class="edge">
<title>12->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M741.1486,-287.8448C739.4304,-268.4464 734.292,-237.5796 719,-216 662.7731,-136.6545 545.4894,-106.7861 478.5795,-95.9143"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="479.1056,-92.4542 468.6884,-94.3861 478.0367,-99.3721 479.1056,-92.4542"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M730.0933,-287.8848C729.3552,-268.5206 725.6888,-237.6828 711,-216 661.6063,-143.0879 558.0766,-111.1912 496.0514,-98.1645"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="496.589,-94.7026 486.095,-96.1605 495.2077,-101.565 496.589,-94.7026"/>
+</g>
+<!-- 13 -->
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M874.027,-468C874.027,-468 727.973,-468 727.973,-468 721.973,-468 715.973,-462 715.973,-456 715.973,-456 715.973,-444 715.973,-444 715.973,-438 721.973,-432 727.973,-432 727.973,-432 874.027,-432 874.027,-432 880.027,-432 886.027,-438 886.027,-444 886.027,-444 886.027,-456 886.027,-456 886.027,-462 880.027,-468 874.027,-468"/>
+<text text-anchor="middle" x="801" y="-447" font-family="sans" font-size="10.00" fill="#000000">sort_genomic_alignment_samtools</text>
</g>
<!-- 13->12 -->
<g id="edge25" class="edge">
<title>13->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M959.3002,-431.9669C973.1458,-423.189 987.3358,-411.2027 995,-396 1002.2027,-381.7129 1005.0639,-372.4386 995,-360 971.9249,-331.4801 875.2729,-317.3695 808.3453,-310.8919"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="808.569,-307.3977 798.2871,-309.9538 807.9188,-314.3674 808.569,-307.3977"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M777.7213,-431.786C767.0771,-422.2438 755.2501,-409.7005 748,-396 737.9069,-376.9272 733.4552,-352.8482 731.5007,-334.3967"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="734.9725,-333.9205 730.6147,-324.2634 727.9991,-334.5302 734.9725,-333.9205"/>
</g>
-<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M973.7629,-396C973.7629,-396 820.2371,-396 820.2371,-396 814.2371,-396 808.2371,-390 808.2371,-384 808.2371,-384 808.2371,-372 808.2371,-372 808.2371,-366 814.2371,-360 820.2371,-360 820.2371,-360 973.7629,-360 973.7629,-360 979.7629,-360 985.7629,-366 985.7629,-372 985.7629,-372 985.7629,-384 985.7629,-384 985.7629,-390 979.7629,-396 973.7629,-396"/>
-<text text-anchor="middle" x="897" y="-375" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M922.7629,-396C922.7629,-396 769.2371,-396 769.2371,-396 763.2371,-396 757.2371,-390 757.2371,-384 757.2371,-384 757.2371,-372 757.2371,-372 757.2371,-366 763.2371,-360 769.2371,-360 769.2371,-360 922.7629,-360 922.7629,-360 928.7629,-360 934.7629,-366 934.7629,-372 934.7629,-372 934.7629,-384 934.7629,-384 934.7629,-390 928.7629,-396 922.7629,-396"/>
+<text text-anchor="middle" x="846" y="-375" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
</g>
-<!-- 13->15 -->
-<g id="edge31" class="edge">
-<title>13->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M915.6914,-431.8314C912.9883,-424.0463 909.7684,-414.7729 906.769,-406.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="909.98,-404.7119 903.3935,-396.4133 903.3673,-407.0081 909.98,-404.7119"/>
+<!-- 13->16 -->
+<g id="edge32" class="edge">
+<title>13->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M812.3554,-431.8314C817.4326,-423.7079 823.5227,-413.9637 829.1176,-405.0118"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="832.1597,-406.7483 834.4917,-396.4133 826.2237,-403.0383 832.1597,-406.7483"/>
</g>
-<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1001.955,-324C1001.955,-324 970.045,-324 970.045,-324 964.045,-324 958.045,-318 958.045,-312 958.045,-312 958.045,-300 958.045,-300 958.045,-294 964.045,-288 970.045,-288 970.045,-288 1001.955,-288 1001.955,-288 1007.955,-288 1013.955,-294 1013.955,-300 1013.955,-300 1013.955,-312 1013.955,-312 1013.955,-318 1007.955,-324 1001.955,-324"/>
-<text text-anchor="middle" x="986" y="-303" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M903.955,-324C903.955,-324 872.045,-324 872.045,-324 866.045,-324 860.045,-318 860.045,-312 860.045,-312 860.045,-300 860.045,-300 860.045,-294 866.045,-288 872.045,-288 872.045,-288 903.955,-288 903.955,-288 909.955,-288 915.955,-294 915.955,-300 915.955,-300 915.955,-312 915.955,-312 915.955,-318 909.955,-324 903.955,-324"/>
+<text text-anchor="middle" x="888" y="-303" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
</g>
-<!-- 13->20 -->
+<!-- 13->21 -->
<g id="edge38" class="edge">
-<title>13->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M980.0909,-433.899C998.6731,-425.7011 1017.2081,-413.6093 1028,-396 1040.5792,-375.4742 1026.9451,-350.5676 1011.9485,-332.1638"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1014.2455,-329.47 1005.0516,-324.2047 1008.9553,-334.0541 1014.2455,-329.47"/>
-</g>
-<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M957.9935,-540C957.9935,-540 886.0065,-540 886.0065,-540 880.0065,-540 874.0065,-534 874.0065,-528 874.0065,-528 874.0065,-516 874.0065,-516 874.0065,-510 880.0065,-504 886.0065,-504 886.0065,-504 957.9935,-504 957.9935,-504 963.9935,-504 969.9935,-510 969.9935,-516 969.9935,-516 969.9935,-528 969.9935,-528 969.9935,-534 963.9935,-540 957.9935,-540"/>
-<text text-anchor="middle" x="922" y="-519" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<title>13->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M870.3499,-431.9268C902.1556,-422.0984 934.8325,-409.2612 944,-396 958.8469,-374.5233 940.0378,-349.2091 920.317,-330.907"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="922.5965,-328.2506 912.7825,-324.2586 917.965,-333.4994 922.5965,-328.2506"/>
</g>
<!-- 14->13 -->
-<g id="edge30" class="edge">
+<g id="edge28" class="edge">
<title>14->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M922,-503.8314C922,-496.131 922,-486.9743 922,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="925.5001,-478.4132 922,-468.4133 918.5001,-478.4133 925.5001,-478.4132"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M753.8976,-503.8314C761.2278,-495.454 770.066,-485.3531 778.0969,-476.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="780.9373,-478.2438 784.8884,-468.4133 775.6693,-473.6343 780.9373,-478.2438"/>
</g>
-<!-- 14->17 -->
-<g id="edge33" class="edge">
-<title>14->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M886.1674,-503.8314C867.5843,-494.4089 844.7011,-482.8062 824.9435,-472.7883"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="826.323,-469.5635 815.8211,-468.1628 823.1573,-475.8069 826.323,-469.5635"/>
-</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1101.1305,-468C1101.1305,-468 1018.8695,-468 1018.8695,-468 1012.8695,-468 1006.8695,-462 1006.8695,-456 1006.8695,-456 1006.8695,-444 1006.8695,-444 1006.8695,-438 1012.8695,-432 1018.8695,-432 1018.8695,-432 1101.1305,-432 1101.1305,-432 1107.1305,-432 1113.1305,-438 1113.1305,-444 1113.1305,-444 1113.1305,-456 1113.1305,-456 1113.1305,-462 1107.1305,-468 1101.1305,-468"/>
-<text text-anchor="middle" x="1060" y="-447" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M899.9935,-612C899.9935,-612 828.0065,-612 828.0065,-612 822.0065,-612 816.0065,-606 816.0065,-600 816.0065,-600 816.0065,-588 816.0065,-588 816.0065,-582 822.0065,-576 828.0065,-576 828.0065,-576 899.9935,-576 899.9935,-576 905.9935,-576 911.9935,-582 911.9935,-588 911.9935,-588 911.9935,-600 911.9935,-600 911.9935,-606 905.9935,-612 899.9935,-612"/>
+<text text-anchor="middle" x="864" y="-591" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
</g>
-<!-- 14->21 -->
-<g id="edge41" class="edge">
-<title>14->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M956.8232,-503.8314C974.8011,-494.4516 996.9203,-482.9112 1016.0616,-472.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1017.9411,-475.8916 1025.1879,-468.1628 1014.7031,-469.6855 1017.9411,-475.8916"/>
+<!-- 15->14 -->
+<g id="edge30" class="edge">
+<title>15->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M832.2049,-575.8314C815.9395,-566.5368 795.9614,-555.1208 778.5949,-545.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="780.2039,-542.0854 769.7849,-540.1628 776.7309,-548.1631 780.2039,-542.0854"/>
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-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M497.5586,-396C497.5586,-396 410.4414,-396 410.4414,-396 404.4414,-396 398.4414,-390 398.4414,-384 398.4414,-384 398.4414,-372 398.4414,-372 398.4414,-366 404.4414,-360 410.4414,-360 410.4414,-360 497.5586,-360 497.5586,-360 503.5586,-360 509.5586,-366 509.5586,-372 509.5586,-372 509.5586,-384 509.5586,-384 509.5586,-390 503.5586,-396 497.5586,-396"/>
-<text text-anchor="middle" x="454" y="-375" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<!-- 15->18 -->
+<g id="edge34" class="edge">
+<title>15->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M864,-575.8314C864,-568.131 864,-558.9743 864,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="867.5001,-550.4132 864,-540.4133 860.5001,-550.4133 867.5001,-550.4132"/>
</g>
-<!-- 14->25 -->
-<g id="edge49" class="edge">
-<title>14->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M874.2459,-510.0692C833.3697,-499.6426 773.0505,-483.7475 721,-468 649.3741,-446.3301 568.0078,-418.4205 514.1193,-399.4667"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="514.9803,-396.0592 504.3855,-396.0354 512.653,-402.661 514.9803,-396.0592"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M999.1305,-468C999.1305,-468 916.8695,-468 916.8695,-468 910.8695,-468 904.8695,-462 904.8695,-456 904.8695,-456 904.8695,-444 904.8695,-444 904.8695,-438 910.8695,-432 916.8695,-432 916.8695,-432 999.1305,-432 999.1305,-432 1005.1305,-432 1011.1305,-438 1011.1305,-444 1011.1305,-444 1011.1305,-456 1011.1305,-456 1011.1305,-462 1005.1305,-468 999.1305,-468"/>
+<text text-anchor="middle" x="958" y="-447" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
</g>
-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1085.0966,-108C1085.0966,-108 1022.9034,-108 1022.9034,-108 1016.9034,-108 1010.9034,-102 1010.9034,-96 1010.9034,-96 1010.9034,-84 1010.9034,-84 1010.9034,-78 1016.9034,-72 1022.9034,-72 1022.9034,-72 1085.0966,-72 1085.0966,-72 1091.0966,-72 1097.0966,-78 1097.0966,-84 1097.0966,-84 1097.0966,-96 1097.0966,-96 1097.0966,-102 1091.0966,-108 1085.0966,-108"/>
-<text text-anchor="middle" x="1054" y="-87" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
+<!-- 15->22 -->
+<g id="edge40" class="edge">
+<title>15->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M888.587,-575.8722C900.2615,-566.2624 913.6664,-553.6354 923,-540 936.0238,-520.9735 945.1556,-496.4147 950.8184,-477.7592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="954.2031,-478.6532 953.6101,-468.075 947.477,-476.7142 954.2031,-478.6532"/>
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-<!-- 14->33 -->
-<g id="edge61" class="edge">
-<title>14->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M969.9053,-514.5502C1021.9209,-505.5388 1100.4722,-488.9387 1122,-468 1151.9364,-438.8828 1149,-419.7612 1149,-378 1149,-378 1149,-378 1149,-234 1149,-186.0912 1111.9087,-141.8312 1084.079,-115.3654"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1086.2364,-112.5938 1076.5137,-108.3843 1081.4892,-117.7382 1086.2364,-112.5938"/>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M523.5586,-396C523.5586,-396 436.4414,-396 436.4414,-396 430.4414,-396 424.4414,-390 424.4414,-384 424.4414,-384 424.4414,-372 424.4414,-372 424.4414,-366 430.4414,-360 436.4414,-360 436.4414,-360 523.5586,-360 523.5586,-360 529.5586,-360 535.5586,-366 535.5586,-372 535.5586,-372 535.5586,-384 535.5586,-384 535.5586,-390 529.5586,-396 523.5586,-396"/>
+<text text-anchor="middle" x="480" y="-375" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
</g>
-<!-- 15->12 -->
-<g id="edge28" class="edge">
-<title>15->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M857.887,-359.8314C837.2488,-350.2446 811.7516,-338.4008 789.9327,-328.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="791.3756,-325.0766 780.8318,-324.038 788.4266,-331.4251 791.3756,-325.0766"/>
+<!-- 15->26 -->
+<g id="edge47" class="edge">
+<title>15->26</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M816.1185,-585.8191C766.0712,-576.3826 691.9512,-559.6218 671,-540 633.8602,-505.2168 668.9634,-467.9982 633,-432 626.2553,-425.2487 583.7776,-410.5133 545.2881,-398.1384"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="546.2036,-394.7567 535.6128,-395.0494 544.0745,-401.4251 546.2036,-394.7567"/>
</g>
-<!-- 15->20 -->
-<g id="edge40" class="edge">
-<title>15->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M919.4585,-359.8314C930.4205,-350.9632 943.7699,-340.1637 955.6265,-330.5718"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="957.9755,-333.1734 963.5487,-324.1628 953.5729,-327.7313 957.9755,-333.1734"/>
+<!-- 34 -->
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M901.0966,-108C901.0966,-108 838.9034,-108 838.9034,-108 832.9034,-108 826.9034,-102 826.9034,-96 826.9034,-96 826.9034,-84 826.9034,-84 826.9034,-78 832.9034,-72 838.9034,-72 838.9034,-72 901.0966,-72 901.0966,-72 907.0966,-72 913.0966,-78 913.0966,-84 913.0966,-84 913.0966,-96 913.0966,-96 913.0966,-102 907.0966,-108 901.0966,-108"/>
+<text text-anchor="middle" x="870" y="-87" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M701.6866,-396C701.6866,-396 578.3134,-396 578.3134,-396 572.3134,-396 566.3134,-390 566.3134,-384 566.3134,-384 566.3134,-372 566.3134,-372 566.3134,-366 572.3134,-360 578.3134,-360 578.3134,-360 701.6866,-360 701.6866,-360 707.6866,-360 713.6866,-366 713.6866,-372 713.6866,-372 713.6866,-384 713.6866,-384 713.6866,-390 707.6866,-396 701.6866,-396"/>
-<text text-anchor="middle" x="640" y="-375" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<!-- 15->34 -->
+<g id="edge61" class="edge">
+<title>15->34</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M911.8195,-578.0834C963.6338,-557.4596 1039,-516.1003 1039,-450 1039,-450 1039,-450 1039,-234 1039,-189.0781 1025.6847,-174.817 993,-144 973.3885,-125.5092 946.4146,-112.7079 922.7233,-104.2278"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="923.7402,-100.8767 913.1457,-100.9651 921.4829,-107.5028 923.7402,-100.8767"/>
</g>
<!-- 16->12 -->
-<g id="edge27" class="edge">
-<title>16->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M665.7389,-359.8314C678.5437,-350.7927 694.1909,-339.7476 707.9719,-330.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="710.118,-332.7891 716.2693,-324.1628 706.0812,-327.0703 710.118,-332.7891"/>
-</g>
-<!-- 17->12 -->
<g id="edge26" class="edge">
-<title>17->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M775.1873,-431.7623C768.6773,-407.0928 757.0047,-362.8598 749.3818,-333.9731"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="752.7094,-332.8656 746.7736,-324.0896 745.9411,-334.6517 752.7094,-332.8656"/>
-</g>
-<!-- 17->15 -->
-<g id="edge32" class="edge">
-<title>17->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M809.524,-431.8314C824.4891,-422.6221 842.8386,-411.3301 858.8603,-401.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="860.8032,-404.3847 867.4854,-396.1628 857.1345,-398.423 860.8032,-404.3847"/>
+<title>16->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M816.7283,-359.8314C801.8912,-350.6221 783.6985,-339.3301 767.8138,-329.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="769.6045,-326.4628 759.2623,-324.1628 765.913,-332.4102 769.6045,-326.4628"/>
</g>
-<!-- 17->20 -->
+<!-- 16->21 -->
<g id="edge39" class="edge">
-<title>17->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M778.7019,-431.6499C778.3213,-411.495 780.9523,-379.417 799,-360 819.1471,-338.3243 899.2594,-321.0315 947.853,-312.2704"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="948.7638,-315.6639 958.0045,-310.4813 947.5488,-308.7702 948.7638,-315.6639"/>
+<title>16->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M856.5984,-359.8314C861.2877,-351.7925 866.9028,-342.1666 872.0798,-333.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="875.2434,-334.8146 877.2589,-324.4133 869.1969,-331.2875 875.2434,-334.8146"/>
</g>
-<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M974,-180C974,-180 944,-180 944,-180 938,-180 932,-174 932,-168 932,-168 932,-156 932,-156 932,-150 938,-144 944,-144 944,-144 974,-144 974,-144 980,-144 986,-150 986,-156 986,-156 986,-168 986,-168 986,-174 980,-180 974,-180"/>
-<text text-anchor="middle" x="959" y="-159" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M688.6866,-396C688.6866,-396 565.3134,-396 565.3134,-396 559.3134,-396 553.3134,-390 553.3134,-384 553.3134,-384 553.3134,-372 553.3134,-372 553.3134,-366 559.3134,-360 565.3134,-360 565.3134,-360 688.6866,-360 688.6866,-360 694.6866,-360 700.6866,-366 700.6866,-372 700.6866,-372 700.6866,-384 700.6866,-384 700.6866,-390 694.6866,-396 688.6866,-396"/>
+<text text-anchor="middle" x="627" y="-375" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
-<!-- 18->1 -->
-<g id="edge12" class="edge">
-<title>18->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M931.9886,-158.3305C847.6931,-146.8791 588.5801,-111.6788 478.8847,-96.7768"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="479.1265,-93.2776 468.7463,-95.3995 478.1841,-100.2139 479.1265,-93.2776"/>
+<!-- 17->12 -->
+<g id="edge27" class="edge">
+<title>17->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M652.9912,-359.8314C665.9216,-350.7927 681.7222,-339.7476 695.6383,-330.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="697.8263,-332.7608 704.0171,-324.1628 693.8157,-327.0235 697.8263,-332.7608"/>
+</g>
+<!-- 18->13 -->
+<g id="edge29" class="edge">
+<title>18->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M848.1024,-503.8314C840.7722,-495.454 831.934,-485.3531 823.9031,-476.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="826.3307,-473.6343 817.1116,-468.4133 821.0627,-478.2438 826.3307,-473.6343"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1108.837,-252C1108.837,-252 999.163,-252 999.163,-252 993.163,-252 987.163,-246 987.163,-240 987.163,-240 987.163,-228 987.163,-228 987.163,-222 993.163,-216 999.163,-216 999.163,-216 1108.837,-216 1108.837,-216 1114.837,-216 1120.837,-222 1120.837,-228 1120.837,-228 1120.837,-240 1120.837,-240 1120.837,-246 1114.837,-252 1108.837,-252"/>
-<text text-anchor="middle" x="1054" y="-231" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M972,-180C972,-180 942,-180 942,-180 936,-180 930,-174 930,-168 930,-168 930,-156 930,-156 930,-150 936,-144 942,-144 942,-144 972,-144 972,-144 978,-144 984,-150 984,-156 984,-156 984,-168 984,-168 984,-174 978,-180 972,-180"/>
+<text text-anchor="middle" x="957" y="-159" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
-<!-- 19->18 -->
-<g id="edge35" class="edge">
-<title>19->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1030.0275,-215.8314C1018.2139,-206.8779 1003.8028,-195.9558 991.0565,-186.2955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="993.0486,-183.4137 982.9648,-180.1628 988.8205,-188.9925 993.0486,-183.4137"/>
-</g>
-<!-- 34 -->
-<g id="node35" class="node">
-<title>34</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M1084.4453,-180C1084.4453,-180 1023.5547,-180 1023.5547,-180 1017.5547,-180 1011.5547,-174 1011.5547,-168 1011.5547,-168 1011.5547,-156 1011.5547,-156 1011.5547,-150 1017.5547,-144 1023.5547,-144 1023.5547,-144 1084.4453,-144 1084.4453,-144 1090.4453,-144 1096.4453,-150 1096.4453,-156 1096.4453,-156 1096.4453,-168 1096.4453,-168 1096.4453,-174 1090.4453,-180 1084.4453,-180"/>
-<text text-anchor="middle" x="1054" y="-159" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<!-- 19->1 -->
+<g id="edge10" class="edge">
+<title>19->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M929.8892,-147.2117C926.9454,-145.9802 923.9476,-144.8745 921,-144 842.1672,-120.6106 600.7893,-101.0768 495.7262,-93.443"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="495.9207,-89.948 485.695,-92.7203 495.4176,-96.9299 495.9207,-89.948"/>
</g>
-<!-- 19->34 -->
-<g id="edge63" class="edge">
-<title>19->34</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1054,-215.8314C1054,-208.131 1054,-198.9743 1054,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1057.5001,-190.4132 1054,-180.4133 1050.5001,-190.4133 1057.5001,-190.4132"/>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M942.837,-252C942.837,-252 833.163,-252 833.163,-252 827.163,-252 821.163,-246 821.163,-240 821.163,-240 821.163,-228 821.163,-228 821.163,-222 827.163,-216 833.163,-216 833.163,-216 942.837,-216 942.837,-216 948.837,-216 954.837,-222 954.837,-228 954.837,-228 954.837,-240 954.837,-240 954.837,-246 948.837,-252 942.837,-252"/>
+<text text-anchor="middle" x="888" y="-231" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
</g>
<!-- 20->19 -->
-<g id="edge37" class="edge">
+<g id="edge35" class="edge">
<title>20->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1003.1593,-287.8314C1011.1511,-279.3694 1020.8038,-269.1489 1029.5416,-259.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1032.288,-262.0866 1036.6097,-252.4133 1027.1989,-257.2802 1032.288,-262.0866"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M905.4116,-215.8314C913.521,-207.3694 923.3156,-197.1489 932.182,-187.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="934.9618,-190.0549 939.354,-180.4133 929.9079,-185.2115 934.9618,-190.0549"/>
</g>
-<!-- 21->18 -->
-<g id="edge36" class="edge">
-<title>21->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1057.3783,-431.9539C1054.5891,-413.6993 1049.7855,-384.7241 1044,-360 1036.4051,-327.5434 1041.5433,-315.6994 1023,-288 1008.7518,-266.7165 991.4322,-273.8077 978,-252 966.5351,-233.3863 961.8987,-208.9441 960.0662,-190.2295"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="963.5536,-189.9297 959.2958,-180.2281 956.5743,-190.4674 963.5536,-189.9297"/>
+<!-- 35 -->
+<g id="node36" class="node">
+<title>35</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M900.4453,-180C900.4453,-180 839.5547,-180 839.5547,-180 833.5547,-180 827.5547,-174 827.5547,-168 827.5547,-168 827.5547,-156 827.5547,-156 827.5547,-150 833.5547,-144 839.5547,-144 839.5547,-144 900.4453,-144 900.4453,-144 906.4453,-144 912.4453,-150 912.4453,-156 912.4453,-156 912.4453,-168 912.4453,-168 912.4453,-174 906.4453,-180 900.4453,-180"/>
+<text text-anchor="middle" x="870" y="-159" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
</g>
-<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M451.9209,-180C451.9209,-180 406.0791,-180 406.0791,-180 400.0791,-180 394.0791,-174 394.0791,-168 394.0791,-168 394.0791,-156 394.0791,-156 394.0791,-150 400.0791,-144 406.0791,-144 406.0791,-144 451.9209,-144 451.9209,-144 457.9209,-144 463.9209,-150 463.9209,-156 463.9209,-156 463.9209,-168 463.9209,-168 463.9209,-174 457.9209,-180 451.9209,-180"/>
-<text text-anchor="middle" x="429" y="-159" font-family="sans" font-size="10.00" fill="#000000">pca_salmon</text>
+<!-- 20->35 -->
+<g id="edge62" class="edge">
+<title>20->35</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M883.4578,-215.8314C881.5116,-208.0463 879.1932,-198.7729 877.0337,-190.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="880.4242,-189.2658 874.6033,-180.4133 873.6332,-190.9636 880.4242,-189.2658"/>
</g>
-<!-- 22->1 -->
-<g id="edge14" class="edge">
-<title>22->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M429,-143.8314C429,-136.131 429,-126.9743 429,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="432.5001,-118.4132 429,-108.4133 425.5001,-118.4133 432.5001,-118.4132"/>
+<!-- 21->20 -->
+<g id="edge37" class="edge">
+<title>21->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M888,-287.8314C888,-280.131 888,-270.9743 888,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="891.5001,-262.4132 888,-252.4133 884.5001,-262.4133 891.5001,-262.4132"/>
+</g>
+<!-- 22->19 -->
+<g id="edge36" class="edge">
+<title>22->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M959.5825,-431.7736C962.7592,-392.3646 969.1827,-296.2969 964,-216 963.4605,-207.6422 962.4561,-198.6019 961.3732,-190.3525"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="964.838,-189.8568 959.9885,-180.437 957.9053,-190.825 964.838,-189.8568"/>
</g>
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M521.9746,-252C521.9746,-252 406.0254,-252 406.0254,-252 400.0254,-252 394.0254,-246 394.0254,-240 394.0254,-240 394.0254,-228 394.0254,-228 394.0254,-222 400.0254,-216 406.0254,-216 406.0254,-216 521.9746,-216 521.9746,-216 527.9746,-216 533.9746,-222 533.9746,-228 533.9746,-228 533.9746,-240 533.9746,-240 533.9746,-246 527.9746,-252 521.9746,-252"/>
-<text text-anchor="middle" x="464" y="-231" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M581.9209,-180C581.9209,-180 536.0791,-180 536.0791,-180 530.0791,-180 524.0791,-174 524.0791,-168 524.0791,-168 524.0791,-156 524.0791,-156 524.0791,-150 530.0791,-144 536.0791,-144 536.0791,-144 581.9209,-144 581.9209,-144 587.9209,-144 593.9209,-150 593.9209,-156 593.9209,-156 593.9209,-168 593.9209,-168 593.9209,-174 587.9209,-180 581.9209,-180"/>
+<text text-anchor="middle" x="559" y="-159" font-family="sans" font-size="10.00" fill="#000000">pca_salmon</text>
</g>
-<!-- 23->0 -->
-<g id="edge2" class="edge">
-<title>23->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M534.0551,-216.5212C567.1209,-206.7127 601.4297,-193.7111 611,-180 642.4505,-134.9413 593.0504,-76.1333 558.3236,-43.1921"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="560.4564,-40.3974 550.7375,-36.1791 555.7046,-45.5375 560.4564,-40.3974"/>
+<!-- 23->1 -->
+<g id="edge11" class="edge">
+<title>23->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M530.4853,-143.8314C516.1658,-134.7074 498.6376,-123.539 483.2662,-113.7449"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="484.8199,-110.5847 474.5055,-108.1628 481.0583,-116.4882 484.8199,-110.5847"/>
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-<!-- 23->22 -->
-<g id="edge43" class="edge">
-<title>23->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M455.168,-215.8314C451.3014,-207.8771 446.6794,-198.369 442.4032,-189.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="445.4707,-187.8768 437.9509,-180.4133 439.1751,-190.9371 445.4707,-187.8768"/>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M689.9746,-252C689.9746,-252 574.0254,-252 574.0254,-252 568.0254,-252 562.0254,-246 562.0254,-240 562.0254,-240 562.0254,-228 562.0254,-228 562.0254,-222 568.0254,-216 574.0254,-216 574.0254,-216 689.9746,-216 689.9746,-216 695.9746,-216 701.9746,-222 701.9746,-228 701.9746,-228 701.9746,-240 701.9746,-240 701.9746,-246 695.9746,-252 689.9746,-252"/>
+<text text-anchor="middle" x="632" y="-231" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+</g>
+<!-- 24->0 -->
+<g id="edge6" class="edge">
+<title>24->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M633.72,-215.826C635.8106,-184.0072 636.0085,-117.2922 607,-72 597.8634,-57.7347 583.5343,-45.9305 569.9819,-37.0349"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="571.5922,-33.9149 561.2506,-31.6126 567.8992,-39.8616 571.5922,-33.9149"/>
</g>
<!-- 24->23 -->
-<g id="edge45" class="edge">
+<g id="edge42" class="edge">
<title>24->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M564.1861,-287.8314C546.7293,-278.4516 525.2513,-266.9112 506.6648,-256.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="508.2686,-253.8129 497.803,-252.1628 504.9554,-259.9792 508.2686,-253.8129"/>
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-<!-- 28 -->
-<g id="node29" class="node">
-<title>28</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M698.3516,-252C698.3516,-252 563.6484,-252 563.6484,-252 557.6484,-252 551.6484,-246 551.6484,-240 551.6484,-240 551.6484,-228 551.6484,-228 551.6484,-222 557.6484,-216 563.6484,-216 563.6484,-216 698.3516,-216 698.3516,-216 704.3516,-216 710.3516,-222 710.3516,-228 710.3516,-228 710.3516,-240 710.3516,-240 710.3516,-246 704.3516,-252 698.3516,-252"/>
-<text text-anchor="middle" x="631" y="-231" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-</g>
-<!-- 24->28 -->
-<g id="edge54" class="edge">
-<title>24->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M606.3273,-287.8314C609.973,-279.8771 614.3309,-270.369 618.3627,-261.5723"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M613.579,-215.8314C604.8471,-207.219 594.2683,-196.7851 584.7577,-187.4048"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="586.9925,-184.6931 577.4151,-180.1628 582.077,-189.6769 586.9925,-184.6931"/>
</g>
<!-- 25->24 -->
-<g id="edge47" class="edge">
+<g id="edge44" class="edge">
<title>25->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M490.3373,-359.8314C509.3396,-350.3302 532.7758,-338.6121 552.9252,-328.5374"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M501.1599,-287.8314C524.7732,-278.1162 554.0202,-266.0831 578.87,-255.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="580.2415,-259.0797 588.1577,-252.038 577.5781,-252.6061 580.2415,-259.0797"/>
</g>
-<!-- 25->27 -->
-<g id="edge51" class="edge">
-<title>25->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M455.2617,-359.8314C455.7965,-352.131 456.4323,-342.9743 457.0266,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="460.52,-334.6317 457.7213,-324.4133 453.5368,-334.1467 460.52,-334.6317"/>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M532.3516,-252C532.3516,-252 397.6484,-252 397.6484,-252 391.6484,-252 385.6484,-246 385.6484,-240 385.6484,-240 385.6484,-228 385.6484,-228 385.6484,-222 391.6484,-216 397.6484,-216 397.6484,-216 532.3516,-216 532.3516,-216 538.3516,-216 544.3516,-222 544.3516,-228 544.3516,-228 544.3516,-240 544.3516,-240 544.3516,-246 538.3516,-252 532.3516,-252"/>
+<text text-anchor="middle" x="465" y="-231" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+</g>
+<!-- 25->29 -->
+<g id="edge53" class="edge">
+<title>25->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M459.0187,-287.8314C459.8743,-280.131 460.8917,-270.9743 461.8426,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="465.3283,-262.7386 462.9541,-252.4133 458.3711,-261.9656 465.3283,-262.7386"/>
</g>
<!-- 26->25 -->
-<g id="edge48" class="edge">
+<g id="edge45" class="edge">
<title>26->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M238.3028,-431.9243C284.3104,-420.4224 343.4273,-405.6432 388.1335,-394.4666"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="389.1652,-397.8165 398.0177,-391.9956 387.4674,-391.0255 389.1652,-397.8165"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M474.1961,-359.8314C471.7092,-352.0463 468.7469,-342.7729 465.9875,-334.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="469.2591,-332.874 462.882,-324.4133 462.591,-335.0041 469.2591,-332.874"/>
</g>
-<!-- 27->23 -->
-<g id="edge44" class="edge">
-<title>27->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M460.2617,-287.8314C460.7965,-280.131 461.4323,-270.9743 462.0266,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="465.52,-262.6317 462.7213,-252.4133 458.5368,-262.1467 465.52,-262.6317"/>
+<!-- 26->28 -->
+<g id="edge51" class="edge">
+<title>26->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M509.2717,-359.8314C524.1088,-350.6221 542.3015,-339.3301 558.1862,-329.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="560.087,-332.4102 566.7377,-324.1628 556.3955,-326.4628 560.087,-332.4102"/>
</g>
-<!-- 27->28 -->
-<g id="edge53" class="edge">
-<title>27->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M502.4029,-287.8314C525.5091,-278.159 554.1038,-266.1891 578.4577,-255.9944"/>
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+<!-- 27->26 -->
+<g id="edge48" class="edge">
+<title>27->26</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M512.8969,-431.8314C507.9326,-423.7079 501.9778,-413.9637 496.5072,-405.0118"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="499.4536,-403.121 491.2526,-396.4133 493.4806,-406.7712 499.4536,-403.121"/>
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-<!-- 28->0 -->
-<g id="edge3" class="edge">
-<title>28->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M634.2764,-215.9608C639.0734,-183.764 644.3372,-115.6899 613,-72 601.064,-55.359 582.2584,-42.5778 565.4641,-33.6375"/>
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+<!-- 28->24 -->
+<g id="edge43" class="edge">
+<title>28->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M605.0843,-287.8314C609.0615,-279.8771 613.8155,-270.369 618.2139,-261.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="621.4517,-262.9228 622.7934,-252.4133 615.1907,-259.7923 621.4517,-262.9228"/>
</g>
-<!-- 28->22 -->
-<g id="edge42" class="edge">
-<title>28->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M575.5095,-215.9253C547.3434,-206.5444 512.4328,-194.6048 473.445,-180.0761"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="474.5833,-176.765 463.991,-176.5319 472.126,-183.3195 474.5833,-176.765"/>
+<!-- 28->29 -->
+<g id="edge52" class="edge">
+<title>28->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M562.9432,-287.8314C546.0323,-278.5368 525.2615,-267.1208 507.2059,-257.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="508.4957,-253.9122 498.0463,-252.1628 505.124,-260.0468 508.4957,-253.9122"/>
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-<!-- 29 -->
-<g id="node30" class="node">
-<title>29</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M303.2514,-180C303.2514,-180 258.7486,-180 258.7486,-180 252.7486,-180 246.7486,-174 246.7486,-168 246.7486,-168 246.7486,-156 246.7486,-156 246.7486,-150 252.7486,-144 258.7486,-144 258.7486,-144 303.2514,-144 303.2514,-144 309.2514,-144 315.2514,-150 315.2514,-156 315.2514,-156 315.2514,-168 315.2514,-168 315.2514,-174 309.2514,-180 303.2514,-180"/>
-<text text-anchor="middle" x="281" y="-159" font-family="sans" font-size="10.00" fill="#000000">pca_kallisto</text>
+<!-- 29->0 -->
+<g id="edge1" class="edge">
+<title>29->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M531.1972,-215.8792C562.1361,-205.9394 594.1166,-193.0153 603,-180 632.9942,-136.0544 590.3106,-76.9832 559.9081,-43.6659"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="562.2711,-41.0692 552.8767,-36.1706 557.1659,-45.8584 562.2711,-41.0692"/>
</g>
-<!-- 29->1 -->
-<g id="edge10" class="edge">
-<title>29->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M315.3262,-145.3008C335.3506,-135.5592 360.8778,-123.1405 382.6667,-112.5405"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="384.2877,-115.6442 391.7489,-108.1222 381.2254,-109.3495 384.2877,-115.6442"/>
+<!-- 29->23 -->
+<g id="edge41" class="edge">
+<title>29->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M488.7202,-215.8314C500.4094,-206.8779 514.6688,-195.9558 527.2809,-186.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="529.4769,-189.0222 535.2874,-180.1628 525.2203,-183.4651 529.4769,-189.0222"/>
</g>
-<!-- 30->0 -->
-<g id="edge4" class="edge">
-<title>30->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M261.6024,-215.8317C244.1784,-197.2294 223.4093,-167.7572 238,-144 292.5845,-55.1232 425.752,-28.786 491.297,-21.0991"/>
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+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M280.2514,-180C280.2514,-180 235.7486,-180 235.7486,-180 229.7486,-180 223.7486,-174 223.7486,-168 223.7486,-168 223.7486,-156 223.7486,-156 223.7486,-150 229.7486,-144 235.7486,-144 235.7486,-144 280.2514,-144 280.2514,-144 286.2514,-144 292.2514,-150 292.2514,-156 292.2514,-156 292.2514,-168 292.2514,-168 292.2514,-174 286.2514,-180 280.2514,-180"/>
+<text text-anchor="middle" x="258" y="-159" font-family="sans" font-size="10.00" fill="#000000">pca_kallisto</text>
</g>
-<!-- 30->29 -->
-<g id="edge55" class="edge">
-<title>30->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M281,-215.8314C281,-208.131 281,-198.9743 281,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="284.5001,-190.4132 281,-180.4133 277.5001,-190.4133 284.5001,-190.4132"/>
+<!-- 30->1 -->
+<g id="edge12" class="edge">
+<title>30->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M292.4821,-148.7941C321.7156,-137.5983 363.9957,-121.4059 396.7867,-108.8476"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="398.1115,-112.0882 406.1983,-105.2432 395.6079,-105.5512 398.1115,-112.0882"/>
</g>
<!-- 31->0 -->
-<g id="edge6" class="edge">
+<g id="edge2" class="edge">
<title>31->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M148.4155,-215.9881C165.321,-181.9355 206.8267,-108.2845 265,-72 302.5067,-48.6059 428.5028,-30.3241 491.9035,-22.3552"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M282.4792,-215.8532C300.5537,-182.8718 343.0018,-112.7503 397,-72 427.0287,-49.3385 467.8011,-34.8873 497.0446,-26.695"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="498.1216,-30.0299 506.8711,-24.0552 496.3054,-23.2696 498.1216,-30.0299"/>
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-<!-- 31->29 -->
-<g id="edge56" class="edge">
-<title>31->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M175.5803,-215.8314C194.3142,-206.2651 217.4493,-194.4514 237.2693,-184.3306"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="239.0916,-187.33 246.406,-179.665 235.9082,-181.0957 239.0916,-187.33"/>
+<!-- 31->30 -->
+<g id="edge55" class="edge">
+<title>31->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M269.2149,-215.8314C267.6106,-208.131 265.703,-198.9743 263.9201,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="267.3021,-189.4892 261.8361,-180.4133 260.4493,-190.9169 267.3021,-189.4892"/>
</g>
-<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M589.9502,-180C589.9502,-180 494.0498,-180 494.0498,-180 488.0498,-180 482.0498,-174 482.0498,-168 482.0498,-168 482.0498,-156 482.0498,-156 482.0498,-150 488.0498,-144 494.0498,-144 494.0498,-144 589.9502,-144 589.9502,-144 595.9502,-144 601.9502,-150 601.9502,-156 601.9502,-156 601.9502,-168 601.9502,-168 601.9502,-174 595.9502,-180 589.9502,-180"/>
-<text text-anchor="middle" x="542" y="-159" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
+<!-- 32->0 -->
+<g id="edge4" class="edge">
+<title>32->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M145.6936,-215.6465C160.9758,-196.0783 187.2283,-165.0675 215,-144 303.9778,-76.5018 433.8082,-40.2749 496.8686,-25.7289"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="497.7751,-29.1125 506.7609,-23.4995 496.2361,-22.2837 497.7751,-29.1125"/>
+</g>
+<!-- 32->30 -->
+<g id="edge54" class="edge">
+<title>32->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M163.7951,-215.8314C180.0605,-206.5368 200.0386,-195.1208 217.4051,-185.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="219.2691,-188.1631 226.2151,-180.1628 215.7961,-182.0854 219.2691,-188.1631"/>
+</g>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M493.9502,-180C493.9502,-180 398.0498,-180 398.0498,-180 392.0498,-180 386.0498,-174 386.0498,-168 386.0498,-168 386.0498,-156 386.0498,-156 386.0498,-150 392.0498,-144 398.0498,-144 398.0498,-144 493.9502,-144 493.9502,-144 499.9502,-144 505.9502,-150 505.9502,-156 505.9502,-156 505.9502,-168 505.9502,-168 505.9502,-174 499.9502,-180 493.9502,-180"/>
+<text text-anchor="middle" x="446" y="-159" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
</g>
-<!-- 32->1 -->
+<!-- 33->1 -->
<g id="edge7" class="edge">
-<title>32->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M513.4853,-143.8314C499.1658,-134.7074 481.6376,-123.539 466.2662,-113.7449"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="467.8199,-110.5847 457.5055,-108.1628 464.0583,-116.4882 467.8199,-110.5847"/>
+<title>33->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M446,-143.8314C446,-136.131 446,-126.9743 446,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="449.5001,-118.4132 446,-108.4133 442.5001,-118.4133 449.5001,-118.4132"/>
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-<!-- 33->0 -->
-<g id="edge1" class="edge">
-<title>33->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1010.5904,-84.0467C909.5978,-70.1963 660.3176,-36.0093 565.9788,-23.0714"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="566.4213,-19.5994 556.0384,-21.7081 565.4701,-26.5345 566.4213,-19.5994"/>
+<!-- 34->0 -->
+<g id="edge3" class="edge">
+<title>34->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M826.7617,-80.7347C760.1071,-66.4515 633.4257,-39.3055 570.8567,-25.8979"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="571.5359,-22.464 561.0245,-23.791 570.0691,-29.3086 571.5359,-22.464"/>
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-<!-- 34->33 -->
-<g id="edge62" class="edge">
-<title>34->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1054,-143.8314C1054,-136.131 1054,-126.9743 1054,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1057.5001,-118.4132 1054,-108.4133 1050.5001,-118.4133 1057.5001,-118.4132"/>
+<!-- 35->34 -->
+<g id="edge60" class="edge">
+<title>35->34</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M870,-143.8314C870,-136.131 870,-126.9743 870,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="873.5001,-118.4132 870,-108.4133 866.5001,-118.4133 873.5001,-118.4132"/>
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diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 58b2e8adda7b06f189309da923c074836f231dff..63b36129f31e2a83d37b1f714da38847fef07eda 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -20,6 +20,7 @@ on installation and usage please see [here](README.md).
- [**create_index_kallisto**](#create_index_kallisto)
- [**extract_transcripts_as_bed12**](#extract_transcripts_as_bed12)
- [**fastqc**](#fastqc)
+ - [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
- [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
- [**star_rpm**](#star_rpm)
- [**rename_star_rpm_for_alfa**](#rename_star_rpm_for_alfa)
@@ -251,6 +252,17 @@ Prepare quality control report for reads library with
- FastQC output directory with report (`.txt`) and figures (`.png`); used in
[**multiqc_report**](#multiqc_report)
+#### `sort_genomic_alignment_samtools`
+
+Sort BAM file with [**SAMtools**](#third-party-software-used).
+
+> Sort a genome aligned BAM file.
+
+- **Input**
+ - Alignemnts file (`.bam`); from [**map_genome_star**](#map_genome_star)
+- **Output**
+ - Alignemnts file (`.bam`); used in [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools) & [**star_rpm**](#star_rpm) & [**calculate_TIN_scores**](#calculate_tin_scores)
+
#### `index_genomic_alignment_samtools`
Index BAM file with [**SAMtools**](#third-party-software-used).
@@ -261,7 +273,7 @@ Index BAM file with [**SAMtools**](#third-party-software-used).
> in a genomic region of interest.
- **Input**
- - Alignemnts file (`.bam`); from [**map_genome_star**](#map_genome_star)
+ - Alignemnts file (`.bam`); from [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
- **Output**
- BAM index file (`.bam.bai`); used in [**star_rpm**](#star_rpm) &
[**calculate_TIN_scores**](#calculate_tin_scores)
@@ -280,7 +292,7 @@ Create stranded bedGraph coverage (`.bg`) with
> assigned to a strand irrespective of its corresponding mate.
- **Input**
- - Alignments file (`.bam`); from [**map_genome_star**](#map_genome_star)
+ - Alignments file (`.bam`); from [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
- BAM index file (`.bam.bai`); from
[**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
- **Output**
@@ -345,7 +357,7 @@ Calculates the Transcript Integrity Number (TIN) for each transcript with
> is below threshold
- **Input**
- - Alignments file (`.bam`); from [**map_genome_star**](#map_genome_star)
+ - Alignments file (`.bam`); from [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
- BAM index file (`.bam.bai`); from
[**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
- Transcript annotations file (12-column `.bed`); from
@@ -617,14 +629,12 @@ Align short reads to reference genome and/or transcriptome with
- `--outFilterMultimapNmax`: maximum number of multiple alignments allowed; if exceeded, read is considered unmapped; specify in sample table column `multimappers`
- **Output**
- Aligned reads file (`.bam`); used in
- [**calculate_TIN_scores**](#calculate_TIN_scores),
- [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
- and [**star_rpm**](#star_rpm)
+ [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools),
- STAR log file
- **Non-configurable & non-default**
- `--outSAMattributes=All`: NH HI AS nM NM MD jM jI MC ch
- - `--outStd=BAM_SortedByCoordinate`: which output will be directed to `STDOUT` (default 'Log')
- - `--outSAMtype=BAM SortedByCoordinate`: type of SAM/BAM output (default SAM)
+ - `--outStd=BAM_Unsorted`: which output will be directed to `STDOUT` (default 'Log')
+ - `--outSAMtype=BAM Unsorted`: type of SAM/BAM output (default SAM)
- `--outSAMattrRGline`: ID:rnaseq_pipeline SM: *sampleID*
#### `quantification_salmon`
diff --git a/tests/input_files/rule_config.yaml b/tests/input_files/rule_config.yaml
index d45c335e3e9b36567f2ae2cdf21b18dc5413abcd..0aff9961cfacc4ac90f45ee763e397f7fa38a42c 100644
--- a/tests/input_files/rule_config.yaml
+++ b/tests/input_files/rule_config.yaml
@@ -49,6 +49,8 @@ create_index_kallisto:
extract_transcripts_as_bed12:
+sort_genomic_alignment_samtools:
+
index_genomic_alignment_samtools:
calculate_TIN_scores:
diff --git a/workflow/Snakefile b/workflow/Snakefile
index a0ec1ace382c62aaa766b5b7eb0009d60c196037..2714fd7344d3110ae751baaa8dd81f431d7885ea 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -646,6 +646,75 @@ rule extract_transcripts_as_bed12:
1> {log.stdout} 2> {log.stderr}"
+current_rule = 'sort_genomic_alignment_samtools'
+rule sort_genomic_alignment_samtools:
+ '''
+ Sort genome bamfile using samtools
+ '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "map_genome",
+ "{sample}.{seqmode}.Aligned.out.bam"),
+
+ output:
+ bam = os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "map_genome",
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
+ prefix_temp_dir = temp(
+ directory(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}.{seqmode}",
+ "sort_genomic_alignment_samtools")
+ )
+ )
+
+ params:
+ cluster_log_path = config["cluster_log_dir"],
+ additional_params = parse_rule_config(
+ rule_config,
+ current_rule=current_rule,
+ immutable=()
+ )
+
+ singularity:
+ "docker://quay.io/biocontainers/samtools:1.3.1--h1b8c3c0_8"
+
+ conda:
+ os.path.join(workflow.basedir, "envs", "samtools.yaml")
+
+ threads: 8
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "samples",
+ "{sample}",
+ current_rule + ".{seqmode}.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "samples",
+ "{sample}",
+ current_rule + ".{seqmode}.stdout.log")
+
+ shell:
+ "(mkdir -p {output.prefix_temp_dir}; \
+ samtools sort \
+ -o {output.bam} \
+ -T {output.prefix_temp_dir} \
+ -@ {threads} \
+ {params.additional_params} \
+ {input.bam}) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
current_rule = 'index_genomic_alignment_samtools'
rule index_genomic_alignment_samtools:
'''
@@ -657,7 +726,8 @@ rule index_genomic_alignment_samtools:
"samples",
"{sample}",
"map_genome",
- "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam")
+
output:
bai = os.path.join(
config["output_dir"],
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 5cf75efd276dd53dbf7c1bd5afabf2f2061abbde..db45e965609b44007f601fd3c5e60853c1156102 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -225,7 +225,7 @@ rule pe_map_genome_star:
"samples",
"{sample}",
"map_genome",
- "{sample}.pe.Aligned.sortedByCoord.out.bam"),
+ "{sample}.pe.Aligned.out.bam"),
logfile = os.path.join(
config["output_dir"],
"samples",
@@ -294,8 +294,8 @@ rule pe_map_genome_star:
--readFilesCommand zcat \
--outFileNamePrefix {params.outFileNamePrefix} \
--outSAMattributes All \
- --outStd BAM_SortedByCoordinate \
- --outSAMtype BAM SortedByCoordinate \
+ --outStd BAM_Unsorted \
+ --outSAMtype BAM Unsorted \
--outSAMattrRGline ID:rnaseq_pipeline SM:{params.sample_id} \
{params.additional_params} \
> {output.bam};) \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 4e9269bf20a78e85ceb2dd62a4ab5d043a2cc54f..f5cf0a82350706a57d2c9ce7e9935d06f2fa22f1 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -175,7 +175,7 @@ rule map_genome_star:
"samples",
"{sample}",
"map_genome",
- "{sample}.se.Aligned.sortedByCoord.out.bam"),
+ "{sample}.se.Aligned.out.bam"),
logfile = os.path.join(
config["output_dir"],
"samples",
@@ -238,8 +238,8 @@ rule map_genome_star:
--readFilesCommand zcat \
--outFileNamePrefix {params.outFileNamePrefix} \
--outSAMattributes All \
- --outStd BAM_SortedByCoordinate \
- --outSAMtype BAM SortedByCoordinate \
+ --outStd BAM_Unsorted \
+ --outSAMtype BAM Unsorted \
--outSAMattrRGline ID:rnaseq_pipeline SM:{params.sample_id} \
{params.additional_params} \
> {output.bam};) \