From c3fffb6c33f60ed36150a933bec76cd6a1321acc Mon Sep 17 00:00:00 2001 From: Maciej Bak <maciej.bak@unibas.ch> Date: Thu, 12 Mar 2020 15:03:36 +0100 Subject: [PATCH] updated DAG and rulegraph --- images/dag_test_workflow.svg | 896 ++++++++++++++++------------------- images/rule_graph.svg | 112 ++--- 2 files changed, 467 insertions(+), 541 deletions(-) diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg index 720c5f0..208139a 100644 --- a/images/dag_test_workflow.svg +++ b/images/dag_test_workflow.svg @@ -1,591 +1,517 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> -<!-- Generated by graphviz version 2.42.3 (20191010.1750) +<!-- Generated by graphviz version 2.38.0 (20140413.2041) --> <!-- Title: snakemake_dag Pages: 1 --> -<svg width="2113pt" height="625pt" - viewBox="0.00 0.00 2112.50 625.00" xmlns="http://www.w3.org/2000/svg" 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class="edge"> -<title>9->0</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1090.6,-73.43C1093.6,-72.94 1096.57,-72.46 1099.5,-72 1225.04,-52.16 1374.5,-32.53 1442.92,-23.76"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.72,-27.19 1453.19,-22.45 1442.83,-20.24 1443.72,-27.19"/> +<g id="edge9" class="edge"><title>9->0</title> +<path fill="none" stroke="grey" stroke-width="2" d="M998.781,-73.7625C1001.89,-73.165 1004.98,-72.5756 1008,-72 1097.25,-55.0116 1202.3,-35.7258 1256.87,-25.7615"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.56,-29.1926 1266.77,-23.9542 1256.31,-22.3063 1257.56,-29.1926"/> </g> <!-- 10 --> -<g id="node11" class="node"> -<title>10</title> -<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1270.5,-108C1270.5,-108 1120.5,-108 1120.5,-108 1114.5,-108 1108.5,-102 1108.5,-96 1108.5,-96 1108.5,-84 1108.5,-84 1108.5,-78 1114.5,-72 1120.5,-72 1120.5,-72 1270.5,-72 1270.5,-72 1276.5,-72 1282.5,-78 1282.5,-84 1282.5,-84 1282.5,-96 1282.5,-96 1282.5,-102 1276.5,-108 1270.5,-108"/> -<text text-anchor="middle" x="1195.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text> -<text text-anchor="middle" x="1195.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text> +<g id="node11" class="node"><title>10</title> +<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1358.5,-324C1358.5,-324 1327.5,-324 1327.5,-324 1321.5,-324 1315.5,-318 1315.5,-312 1315.5,-312 1315.5,-300 1315.5,-300 1315.5,-294 1321.5,-288 1327.5,-288 1327.5,-288 1358.5,-288 1358.5,-288 1364.5,-288 1370.5,-294 1370.5,-300 1370.5,-300 1370.5,-312 1370.5,-312 1370.5,-318 1364.5,-324 1358.5,-324"/> +<text text-anchor="middle" x="1343" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text> </g> <!-- 10->0 --> -<g id="edge10" class="edge"> -<title>10->0</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1264.85,-71.97C1321.11,-58.15 1398.22,-39.21 1443.37,-28.12"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1444.43,-31.46 1453.31,-25.68 1442.76,-24.66 1444.43,-31.46"/> +<g id="edge10" class="edge"><title>10->0</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1346.95,-287.853C1355.25,-248.209 1371.41,-147.802 1342,-72 1337.87,-61.3668 1330.53,-51.5395 1322.8,-43.3091"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1325.24,-40.7972 1315.68,-36.2223 1320.3,-45.758 1325.24,-40.7972"/> +</g> +<!-- 25 --> +<g id="node26" class="node"><title>25</title> +<path fill="none" stroke="#d87d56" stroke-width="2" d="M1489,-252C1489,-252 1383,-252 1383,-252 1377,-252 1371,-246 1371,-240 1371,-240 1371,-228 1371,-228 1371,-222 1377,-216 1383,-216 1383,-216 1489,-216 1489,-216 1495,-216 1501,-222 1501,-228 1501,-228 1501,-240 1501,-240 1501,-246 1495,-252 1489,-252"/> +<text text-anchor="middle" x="1436" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text> +</g> +<!-- 10->25 --> +<g id="edge53" class="edge"><title>10->25</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1365.99,-287.697C1377.81,-278.796 1392.39,-267.823 1405.18,-258.199"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1407.39,-260.915 1413.28,-252.104 1403.18,-255.322 1407.39,-260.915"/> </g> <!-- 11 --> -<g id="node12" class="node"> -<title>11</title> -<path fill="none" stroke="#61d856" stroke-width="2" d="M1574.5,-324C1574.5,-324 1538.5,-324 1538.5,-324 1532.5,-324 1526.5,-318 1526.5,-312 1526.5,-312 1526.5,-300 1526.5,-300 1526.5,-294 1532.5,-288 1538.5,-288 1538.5,-288 1574.5,-288 1574.5,-288 1580.5,-288 1586.5,-294 1586.5,-300 1586.5,-300 1586.5,-312 1586.5,-312 1586.5,-318 1580.5,-324 1574.5,-324"/> -<text text-anchor="middle" x="1556.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text> +<g id="node12" class="node"><title>11</title> +<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1863.5,-324C1863.5,-324 1832.5,-324 1832.5,-324 1826.5,-324 1820.5,-318 1820.5,-312 1820.5,-312 1820.5,-300 1820.5,-300 1820.5,-294 1826.5,-288 1832.5,-288 1832.5,-288 1863.5,-288 1863.5,-288 1869.5,-288 1875.5,-294 1875.5,-300 1875.5,-300 1875.5,-312 1875.5,-312 1875.5,-318 1869.5,-324 1863.5,-324"/> +<text text-anchor="middle" x="1848" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text> </g> <!-- 11->0 --> -<g id="edge11" class="edge"> -<title>11->0</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1552.37,-287.98C1542.96,-249.41 1518.99,-152.46 1496.5,-72 1494.11,-63.44 1491.36,-54.16 1488.82,-45.79"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1492.14,-44.67 1485.87,-36.13 1485.45,-46.72 1492.14,-44.67"/> +<g id="edge11" class="edge"><title>11->0</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1870.6,-287.963C1881.06,-278.635 1892.4,-266.107 1898,-252 1903.91,-237.13 1906.17,-229.758 1898,-216 1829.77,-101.072 1760.57,-114.929 1634,-72 1528.11,-36.0846 1395.31,-24.3556 1331.55,-20.6448"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.38,-17.13 1321.2,-20.0782 1330.99,-24.1196 1331.38,-17.13"/> </g> -<!-- 26 --> -<g id="node27" class="node"> -<title>26</title> -<path fill="none" stroke="#d88d56" stroke-width="2" d="M1794.5,-252C1794.5,-252 1672.5,-252 1672.5,-252 1666.5,-252 1660.5,-246 1660.5,-240 1660.5,-240 1660.5,-228 1660.5,-228 1660.5,-222 1666.5,-216 1672.5,-216 1672.5,-216 1794.5,-216 1794.5,-216 1800.5,-216 1806.5,-222 1806.5,-228 1806.5,-228 1806.5,-240 1806.5,-240 1806.5,-246 1800.5,-252 1794.5,-252"/> -<text text-anchor="middle" x="1733.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text> +<!-- 27 --> +<g id="node28" class="node"><title>27</title> +<path fill="none" stroke="#d87d56" stroke-width="2" d="M1877,-252C1877,-252 1771,-252 1771,-252 1765,-252 1759,-246 1759,-240 1759,-240 1759,-228 1759,-228 1759,-222 1765,-216 1771,-216 1771,-216 1877,-216 1877,-216 1883,-216 1889,-222 1889,-228 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text-anchor="middle" x="2031.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text> +<!-- 14 --> +<g id="node15" class="node"><title>14</title> +<path fill="none" stroke="#d8c356" stroke-width="2" d="M1580.5,-108C1580.5,-108 1499.5,-108 1499.5,-108 1493.5,-108 1487.5,-102 1487.5,-96 1487.5,-96 1487.5,-84 1487.5,-84 1487.5,-78 1493.5,-72 1499.5,-72 1499.5,-72 1580.5,-72 1580.5,-72 1586.5,-72 1592.5,-78 1592.5,-84 1592.5,-84 1592.5,-96 1592.5,-96 1592.5,-102 1586.5,-108 1580.5,-108"/> +<text text-anchor="middle" x="1540" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text> </g> -<!-- 12->28 --> -<g id="edge59" class="edge"> -<title>12->28</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1971.28,-287.7C1981.25,-278.97 1993.51,-268.24 2004.36,-258.75"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="2006.73,-261.32 2011.95,-252.1 2002.12,-256.06 2006.73,-261.32"/> +<!-- 12->14 --> +<g id="edge36" 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stroke-width="2" d="M975.5,-180C975.5,-180 872.5,-180 872.5,-180 866.5,-180 860.5,-174 860.5,-168 860.5,-168 860.5,-156 860.5,-156 860.5,-150 866.5,-144 872.5,-144 872.5,-144 975.5,-144 975.5,-144 981.5,-144 987.5,-150 987.5,-156 987.5,-156 987.5,-168 987.5,-168 987.5,-174 981.5,-180 975.5,-180"/> +<text text-anchor="middle" x="924" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text> </g> -<!-- 14->0 --> -<g id="edge14" class="edge"> -<title>14->0</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1868.06,-143.8C1861.78,-123.19 1848.21,-89.29 1823.5,-72 1774.63,-37.82 1596.27,-24.81 1517.89,-20.67"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1517.68,-17.15 1507.51,-20.14 1517.32,-24.14 1517.68,-17.15"/> -</g> -<!-- 14->15 --> -<g id="edge43" class="edge"> -<title>14->15</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1845.3,-144.59C1829.93,-135.31 1810.5,-123.59 1793.74,-113.47"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1795.11,-110.21 1784.74,-108.04 1791.49,-116.2 1795.11,-110.21"/> -</g> -<!-- 15->0 --> -<g id="edge15" class="edge"> -<title>15->0</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1698.3,-74.24C1643.75,-60.41 1563.86,-40.14 1517.52,-28.39"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1518.16,-24.94 1507.61,-25.87 1516.44,-31.73 1518.16,-24.94"/> +<!-- 15->19 --> +<g id="edge43" class="edge"><title>15->19</title> +<path fill="none" stroke="grey" stroke-width="2" d="M860,-506.151C860,-479.022 860,-424.909 860,-379 860,-379 860,-379 860,-305 860,-264.458 862.112,-252.382 880,-216 884.958,-205.915 892.205,-196.093 899.392,-187.699"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="902.113,-189.907 906.188,-180.127 896.904,-185.232 902.113,-189.907"/> +</g> +<!-- 21 --> +<g id="node22" class="node"><title>21</title> +<path fill="none" stroke="#d8d356" stroke-width="2" d="M1387.5,-468C1387.5,-468 1298.5,-468 1298.5,-468 1292.5,-468 1286.5,-462 1286.5,-456 1286.5,-456 1286.5,-444 1286.5,-444 1286.5,-438 1292.5,-432 1298.5,-432 1298.5,-432 1387.5,-432 1387.5,-432 1393.5,-432 1399.5,-438 1399.5,-444 1399.5,-444 1399.5,-456 1399.5,-456 1399.5,-462 1393.5,-468 1387.5,-468"/> +<text text-anchor="middle" x="1343" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text> +</g> +<!-- 15->21 --> +<g id="edge48" class="edge"><title>15->21</title> +<path fill="none" stroke="grey" stroke-width="2" d="M928.178,-513.266C1020.66,-499.384 1184.83,-474.742 1276.46,-460.988"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1277.08,-464.433 1286.45,-459.488 1276.05,-457.511 1277.08,-464.433"/> </g> <!-- 16 --> -<g id="node17" class="node"> -<title>16</title> -<path fill="none" stroke="#56d8a9" stroke-width="2" d="M975.5,-542.5C975.5,-542.5 847.5,-542.5 847.5,-542.5 841.5,-542.5 835.5,-536.5 835.5,-530.5 835.5,-530.5 835.5,-518.5 835.5,-518.5 835.5,-512.5 841.5,-506.5 847.5,-506.5 847.5,-506.5 975.5,-506.5 975.5,-506.5 981.5,-506.5 987.5,-512.5 987.5,-518.5 987.5,-518.5 987.5,-530.5 987.5,-530.5 987.5,-536.5 981.5,-542.5 975.5,-542.5"/> -<text text-anchor="middle" x="911.5" y="-522" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text> +<g id="node17" class="node"><title>16</title> +<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1112,-252C1112,-252 1028,-252 1028,-252 1022,-252 1016,-246 1016,-240 1016,-240 1016,-228 1016,-228 1016,-222 1022,-216 1028,-216 1028,-216 1112,-216 1112,-216 1118,-216 1124,-222 1124,-228 1124,-228 1124,-240 1124,-240 1124,-246 1118,-252 1112,-252"/> +<text text-anchor="middle" x="1070" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text> </g> <!-- 16->3 --> -<g id="edge16" class="edge"> -<title>16->3</title> -<path fill="none" stroke="grey" stroke-width="2" d="M902.6,-506.22C889.74,-479.63 867.5,-426.73 867.5,-379 867.5,-379 867.5,-379 867.5,-305 867.5,-264.5 856.77,-218.63 848.84,-190.26"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="852.1,-188.93 845.96,-180.29 845.37,-190.87 852.1,-188.93"/> +<g id="edge16" class="edge"><title>16->3</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1015.75,-218.165C1012.79,-217.418 1009.86,-216.692 1007,-216 956.065,-203.694 898.887,-191.375 852.28,-181.715"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="852.7,-178.228 842.199,-179.632 851.284,-185.083 852.7,-178.228"/> </g> -<!-- 19 --> -<g id="node20" class="node"> -<title>19</title> -<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1481,-468C1481,-468 1380,-468 1380,-468 1374,-468 1368,-462 1368,-456 1368,-456 1368,-444 1368,-444 1368,-438 1374,-432 1380,-432 1380,-432 1481,-432 1481,-432 1487,-432 1493,-438 1493,-444 1493,-444 1493,-456 1493,-456 1493,-462 1487,-468 1481,-468"/> -<text text-anchor="middle" x="1430.5" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text> +<!-- 16->4 --> +<g id="edge18" class="edge"><title>16->4</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1104.25,-215.876C1123.06,-206.469 1146.58,-194.708 1166.67,-184.667"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1168.24,-187.792 1175.62,-180.19 1165.11,-181.531 1168.24,-187.792"/> </g> -<!-- 16->19 --> -<g id="edge48" class="edge"> -<title>16->19</title> -<path fill="none" stroke="grey" stroke-width="2" d="M987.52,-512.88C1086.91,-499 1259.83,-474.84 1357.63,-461.18"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1358.31,-464.62 1367.73,-459.77 1357.34,-457.69 1358.31,-464.62"/> +<!-- 17 --> +<g id="node18" class="node"><title>17</title> +<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1238,-542.5C1238,-542.5 1142,-542.5 1142,-542.5 1136,-542.5 1130,-536.5 1130,-530.5 1130,-530.5 1130,-518.5 1130,-518.5 1130,-512.5 1136,-506.5 1142,-506.5 1142,-506.5 1238,-506.5 1238,-506.5 1244,-506.5 1250,-512.5 1250,-518.5 1250,-518.5 1250,-530.5 1250,-530.5 1250,-536.5 1244,-542.5 1238,-542.5"/> +<text text-anchor="middle" x="1190" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text> </g> -<!-- 24 --> -<g id="node25" class="node"> -<title>24</title> -<path fill="none" stroke="#d86656" stroke-width="2" d="M1082.5,-180C1082.5,-180 964.5,-180 964.5,-180 958.5,-180 952.5,-174 952.5,-168 952.5,-168 952.5,-156 952.5,-156 952.5,-150 958.5,-144 964.5,-144 964.5,-144 1082.5,-144 1082.5,-144 1088.5,-144 1094.5,-150 1094.5,-156 1094.5,-156 1094.5,-168 1094.5,-168 1094.5,-174 1088.5,-180 1082.5,-180"/> -<text text-anchor="middle" x="1023.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text> +<!-- 17->4 --> +<g id="edge17" class="edge"><title>17->4</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1190,-506.151C1190,-479.022 1190,-424.909 1190,-379 1190,-379 1190,-379 1190,-305 1190,-264.822 1197.95,-218.869 1203.82,-190.389"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1207.3,-190.887 1205.95,-180.378 1200.45,-189.431 1207.3,-190.887"/> </g> -<!-- 16->24 --> -<g id="edge53" class="edge"> -<title>16->24</title> -<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-506.15C911.5,-479.02 911.5,-424.91 911.5,-379 911.5,-379 911.5,-379 911.5,-305 911.5,-264.55 906.62,-248.64 930.5,-216 939.95,-203.08 953.57,-192.86 967.48,-184.97"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="969.43,-187.9 976.63,-180.13 966.15,-181.72 969.43,-187.9"/> +<!-- 20 --> +<g id="node21" class="node"><title>20</title> +<path fill="none" stroke="#d89c56" stroke-width="2" d="M1104.5,-180C1104.5,-180 1017.5,-180 1017.5,-180 1011.5,-180 1005.5,-174 1005.5,-168 1005.5,-168 1005.5,-156 1005.5,-156 1005.5,-150 1011.5,-144 1017.5,-144 1017.5,-144 1104.5,-144 1104.5,-144 1110.5,-144 1116.5,-150 1116.5,-156 1116.5,-156 1116.5,-168 1116.5,-168 1116.5,-174 1110.5,-180 1104.5,-180"/> +<text text-anchor="middle" x="1061" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text> </g> -<!-- 17 --> -<g id="node18" class="node"> -<title>17</title> -<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1049,-252C1049,-252 952,-252 952,-252 946,-252 940,-246 940,-240 940,-240 940,-228 940,-228 940,-222 946,-216 952,-216 952,-216 1049,-216 1049,-216 1055,-216 1061,-222 1061,-228 1061,-228 1061,-240 1061,-240 1061,-246 1055,-252 1049,-252"/> -<text text-anchor="middle" x="1000.5" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text> +<!-- 17->20 --> +<g id="edge45" class="edge"><title>17->20</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1182.31,-506.093C1171.21,-479.328 1152,-426.21 1152,-379 1152,-379 1152,-379 1152,-305 1152,-264.553 1154.94,-249.98 1133,-216 1125.28,-204.038 1113.84,-193.843 1102.35,-185.685"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1104.28,-182.765 1094.02,-180.109 1100.39,-188.581 1104.28,-182.765"/> </g> -<!-- 17->3 --> -<g id="edge17" class="edge"> -<title>17->3</title> -<path fill="none" stroke="grey" stroke-width="2" d="M961.36,-215.88C939.49,-206.31 912.04,-194.3 888.84,-184.15"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="890.08,-180.87 879.51,-180.07 887.27,-187.28 890.08,-180.87"/> +<!-- 23 --> +<g id="node24" class="node"><title>23</title> +<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1753.5,-468C1753.5,-468 1680.5,-468 1680.5,-468 1674.5,-468 1668.5,-462 1668.5,-456 1668.5,-456 1668.5,-444 1668.5,-444 1668.5,-438 1674.5,-432 1680.5,-432 1680.5,-432 1753.5,-432 1753.5,-432 1759.5,-432 1765.5,-438 1765.5,-444 1765.5,-444 1765.5,-456 1765.5,-456 1765.5,-462 1759.5,-468 1753.5,-468"/> +<text text-anchor="middle" x="1717" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text> </g> -<!-- 17->4 --> -<g id="edge19" class="edge"> -<title>17->4</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1061.04,-217.91C1063.9,-217.25 1066.73,-216.61 1069.5,-216 1128.09,-203.08 1194.15,-190.17 1246.49,-180.33"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1247.25,-183.75 1256.44,-178.46 1245.96,-176.87 1247.25,-183.75"/> +<!-- 17->23 --> +<g id="edge51" class="edge"><title>17->23</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1250.2,-515.219C1352.16,-501.192 1557.56,-472.934 1658.42,-459.059"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1659,-462.512 1668.43,-457.682 1658.05,-455.577 1659,-462.512"/> </g> <!-- 18 --> -<g id="node19" class="node"> -<title>18</title> -<path fill="none" stroke="#d87d56" stroke-width="2" d="M1321.5,-542.5C1321.5,-542.5 1211.5,-542.5 1211.5,-542.5 1205.5,-542.5 1199.5,-536.5 1199.5,-530.5 1199.5,-530.5 1199.5,-518.5 1199.5,-518.5 1199.5,-512.5 1205.5,-506.5 1211.5,-506.5 1211.5,-506.5 1321.5,-506.5 1321.5,-506.5 1327.5,-506.5 1333.5,-512.5 1333.5,-518.5 1333.5,-518.5 1333.5,-530.5 1333.5,-530.5 1333.5,-536.5 1327.5,-542.5 1321.5,-542.5"/> -<text text-anchor="middle" x="1266.5" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text> -</g> -<!-- 18->4 --> -<g id="edge18" class="edge"> -<title>18->4</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-506.15C1266.5,-479.02 1266.5,-424.91 1266.5,-379 1266.5,-379 1266.5,-379 1266.5,-305 1266.5,-259.77 1296.62,-214.85 1318.68,-188"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1321.44,-190.16 1325.23,-180.27 1316.09,-185.64 1321.44,-190.16"/> +<g id="node19" class="node"><title>18</title> +<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1607,-252C1607,-252 1531,-252 1531,-252 1525,-252 1519,-246 1519,-240 1519,-240 1519,-228 1519,-228 1519,-222 1525,-216 1531,-216 1531,-216 1607,-216 1607,-216 1613,-216 1619,-222 1619,-228 1619,-228 1619,-240 1619,-240 1619,-246 1613,-252 1607,-252"/> +<text text-anchor="middle" x="1569" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text> +</g> +<!-- 18->5 --> +<g id="edge19" class="edge"><title>18->5</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1535,-215.876C1516.4,-206.512 1493.17,-194.814 1473.29,-184.803"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1474.64,-181.562 1464.13,-180.19 1471.49,-187.814 1474.64,-181.562"/> +</g> +<!-- 19->6 --> +<g id="edge20" class="edge"><title>19->6</title> +<path fill="none" stroke="grey" stroke-width="2" d="M963.385,-143.876C985.395,-134.307 1013.01,-122.3 1036.36,-112.148"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1037.97,-115.265 1045.74,-108.068 1035.18,-108.846 1037.97,-115.265"/> +</g> +<!-- 19->7 --> +<g id="edge22" class="edge"><title>19->7</title> +<path fill="none" stroke="grey" stroke-width="2" d="M987.686,-146.1C990.834,-145.385 993.952,-144.682 997,-144 1051.64,-131.776 1113.21,-118.563 1161.21,-108.387"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1162.19,-111.759 1171.24,-106.264 1160.74,-104.911 1162.19,-111.759"/> +</g> 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stroke-width="2" d="M1418,-396C1418,-396 1268,-396 1268,-396 1262,-396 1256,-390 1256,-384 1256,-384 1256,-372 1256,-372 1256,-366 1262,-360 1268,-360 1268,-360 1418,-360 1418,-360 1424,-360 1430,-366 1430,-372 1430,-372 1430,-384 1430,-384 1430,-390 1424,-396 1418,-396"/> +<text text-anchor="middle" x="1343" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text> +<text text-anchor="middle" x="1343" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text> </g> -<!-- 18->22 --> -<g id="edge51" class="edge"> -<title>18->22</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1333.73,-514.93C1444.4,-500.83 1663.5,-472.92 1771.81,-459.11"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.46,-462.56 1781.94,-457.82 1771.58,-455.62 1772.46,-462.56"/> +<!-- 21->22 --> +<g id="edge49" class="edge"><title>21->22</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1343,-431.697C1343,-423.983 1343,-414.712 1343,-406.112"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-406.104 1343,-396.104 1339.5,-406.104 1346.5,-406.104"/> </g> -<!-- 25 --> -<g id="node26" class="node"> -<title>25</title> -<path fill="none" stroke="#97d856" stroke-width="2" d="M1226,-180C1226,-180 1125,-180 1125,-180 1119,-180 1113,-174 1113,-168 1113,-168 1113,-156 1113,-156 1113,-150 1119,-144 1125,-144 1125,-144 1226,-144 1226,-144 1232,-144 1238,-150 1238,-156 1238,-156 1238,-168 1238,-168 1238,-174 1232,-180 1226,-180"/> -<text text-anchor="middle" x="1175.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text> -</g> -<!-- 18->25 --> -<g id="edge55" class="edge"> -<title>18->25</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1258.81,-506.09C1247.71,-479.33 1228.5,-426.21 1228.5,-379 1228.5,-379 1228.5,-379 1228.5,-305 1228.5,-264.46 1223.88,-253.51 1208.5,-216 1204.7,-206.72 1199.33,-197.22 1194.03,-188.88"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1196.82,-186.75 1188.38,-180.34 1190.98,-190.62 1196.82,-186.75"/> -</g> -<!-- 19->5 --> -<g id="edge20" class="edge"> -<title>19->5</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1368.25,-431.95C1350.75,-423.98 1333.72,-412.47 1323.5,-396 1315.06,-382.41 1314.85,-373.46 1323.5,-360 1334.35,-343.11 1352.07,-331.53 1370.43,-323.63"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1371.76,-326.87 1379.76,-319.93 1369.18,-320.36 1371.76,-326.87"/> -</g> -<!-- 19->11 --> -<g id="edge34" class="edge"> -<title>19->11</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1487.66,-431.93C1506.05,-423.8 1524.91,-412.21 1537.5,-396 1551.1,-378.5 1555.5,-353.46 1556.7,-334.4"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1560.2,-334.36 1557.08,-324.24 1553.21,-334.1 1560.2,-334.36"/> +<!-- 31 --> +<g id="node32" class="node"><title>31</title> +<path fill="none" stroke="#b6d856" stroke-width="2" d="M1520,-324C1520,-324 1432,-324 1432,-324 1426,-324 1420,-318 1420,-312 1420,-312 1420,-300 1420,-300 1420,-294 1426,-288 1432,-288 1432,-288 1520,-288 1520,-288 1526,-288 1532,-294 1532,-300 1532,-300 1532,-312 1532,-312 1532,-318 1526,-324 1520,-324"/> +<text text-anchor="middle" x="1476" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text> +</g> +<!-- 21->31 --> +<g id="edge56" class="edge"><title>21->31</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1387.92,-431.937C1405.7,-423.364 1425.16,-411.461 1439,-396 1454.73,-378.433 1464.35,-353.241 1469.82,-334.14"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1473.27,-334.805 1472.45,-324.242 1466.5,-333.01 1473.27,-334.805"/> +</g> +<!-- 22->10 --> +<g id="edge29" class="edge"><title>22->10</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1343,-359.697C1343,-351.983 1343,-342.712 1343,-334.112"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-334.104 1343,-324.104 1339.5,-334.104 1346.5,-334.104"/> +</g> +<!-- 22->31 --> +<g id="edge57" class="edge"><title>22->31</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1375.54,-359.876C1393.25,-350.554 1415.35,-338.919 1434.32,-328.939"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1436.12,-331.944 1443.34,-324.19 1432.86,-325.75 1436.12,-331.944"/> +</g> +<!-- 23->11 --> +<g id="edge30" class="edge"><title>23->11</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1765.69,-446.525C1801.26,-441.86 1847.27,-429.261 1871,-396 1884.22,-377.466 1875.57,-351.952 1865.31,-332.991"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1868.29,-331.152 1860.23,-324.269 1862.24,-334.673 1868.29,-331.152"/> </g> -<!-- 20 --> -<g id="node21" class="node"> -<title>20</title> -<path fill="none" stroke="#d8a456" stroke-width="2" d="M1516.5,-396C1516.5,-396 1344.5,-396 1344.5,-396 1338.5,-396 1332.5,-390 1332.5,-384 1332.5,-384 1332.5,-372 1332.5,-372 1332.5,-366 1338.5,-360 1344.5,-360 1344.5,-360 1516.5,-360 1516.5,-360 1522.5,-360 1528.5,-366 1528.5,-372 1528.5,-372 1528.5,-384 1528.5,-384 1528.5,-390 1522.5,-396 1516.5,-396"/> -<text text-anchor="middle" x="1430.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text> -<text text-anchor="middle" x="1430.5" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text> -</g> -<!-- 19->20 --> -<g id="edge49" class="edge"> -<title>19->20</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1430.5,-431.7C1430.5,-423.98 1430.5,-414.71 1430.5,-406.11"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1434,-406.1 1430.5,-396.1 1427,-406.1 1434,-406.1"/> -</g> -<!-- 20->5 --> -<g id="edge21" class="edge"> -<title>20->5</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1432.72,-359.7C1433.72,-351.98 1434.91,-342.71 1436.01,-334.11"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1439.5,-334.47 1437.3,-324.1 1432.55,-333.58 1439.5,-334.47"/> -</g> -<!-- 20->11 --> -<g id="edge35" class="edge"> -<title>20->11</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1461.32,-359.88C1478.2,-350.5 1499.28,-338.79 1517.32,-328.77"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1519.39,-331.62 1526.43,-323.71 1515.99,-325.5 1519.39,-331.62"/> +<!-- 24 --> +<g id="node25" class="node"><title>24</title> +<path fill="none" stroke="#d88d56" stroke-width="2" d="M1850,-396C1850,-396 1700,-396 1700,-396 1694,-396 1688,-390 1688,-384 1688,-384 1688,-372 1688,-372 1688,-366 1694,-360 1700,-360 1700,-360 1850,-360 1850,-360 1856,-360 1862,-366 1862,-372 1862,-372 1862,-384 1862,-384 1862,-390 1856,-396 1850,-396"/> +<text text-anchor="middle" x="1775" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text> +<text text-anchor="middle" x="1775" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text> </g> -<!-- 21 --> -<g id="node22" class="node"> -<title>21</title> -<path fill="none" stroke="#d6d856" stroke-width="2" d="M1732.5,-396C1732.5,-396 1596.5,-396 1596.5,-396 1590.5,-396 1584.5,-390 1584.5,-384 1584.5,-384 1584.5,-372 1584.5,-372 1584.5,-366 1590.5,-360 1596.5,-360 1596.5,-360 1732.5,-360 1732.5,-360 1738.5,-360 1744.5,-366 1744.5,-372 1744.5,-372 1744.5,-384 1744.5,-384 1744.5,-390 1738.5,-396 1732.5,-396"/> -<text text-anchor="middle" x="1664.5" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text> -</g> -<!-- 21->5 --> -<g id="edge22" class="edge"> -<title>21->5</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1609.75,-359.97C1577.9,-350.06 1537.58,-337.51 1504.17,-327.12"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1505.09,-323.74 1494.5,-324.11 1503.01,-330.42 1505.09,-323.74"/> -</g> -<!-- 21->6 --> -<g id="edge25" class="edge"> -<title>21->6</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1677.85,-359.7C1684.26,-351.39 1692.06,-341.28 1699.11,-332.14"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1701.97,-334.16 1705.31,-324.1 1696.43,-329.88 1701.97,-334.16"/> -</g> -<!-- 22->6 --> -<g id="edge23" class="edge"> -<title>22->6</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1821.21,-431.84C1812.59,-421.47 1801.4,-407.99 1791.5,-396 1773.79,-374.54 1753.76,-350.1 1739.16,-332.27"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1741.51,-329.61 1732.46,-324.09 1736.09,-334.04 1741.51,-329.61"/> -</g> -<!-- 22->12 --> -<g id="edge36" class="edge"> -<title>22->12</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1889.09,-448.07C1928.28,-444.23 1979.03,-431.98 2005.5,-396 2020.98,-374.96 2001.77,-349.31 1982.1,-330.96"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1984.41,-328.33 1974.61,-324.31 1979.77,-333.57 1984.41,-328.33"/> +<!-- 23->24 --> +<g id="edge52" class="edge"><title>23->24</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1731.34,-431.697C1738.29,-423.305 1746.77,-413.07 1754.4,-403.861"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1757.14,-406.038 1760.83,-396.104 1751.75,-401.571 1757.14,-406.038"/> </g> -<!-- 23 --> -<g id="node24" class="node"> -<title>23</title> -<path fill="none" stroke="#d8a456" stroke-width="2" d="M1984.5,-396C1984.5,-396 1812.5,-396 1812.5,-396 1806.5,-396 1800.5,-390 1800.5,-384 1800.5,-384 1800.5,-372 1800.5,-372 1800.5,-366 1806.5,-360 1812.5,-360 1812.5,-360 1984.5,-360 1984.5,-360 1990.5,-360 1996.5,-366 1996.5,-372 1996.5,-372 1996.5,-384 1996.5,-384 1996.5,-390 1990.5,-396 1984.5,-396"/> -<text text-anchor="middle" x="1898.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text> -<text text-anchor="middle" x="1898.5" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text> -</g> -<!-- 22->23 --> -<g id="edge52" class="edge"> -<title>22->23</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1851.07,-431.7C1858.7,-423.22 1868.02,-412.86 1876.38,-403.58"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.02,-405.88 1883.11,-396.1 1873.81,-401.2 1879.02,-405.88"/> -</g> -<!-- 23->6 --> -<g id="edge24" class="edge"> -<title>23->6</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1854.47,-359.88C1829.53,-350.18 1798.16,-337.98 1771.84,-327.74"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.98,-324.43 1762.39,-324.07 1770.44,-330.95 1772.98,-324.43"/> -</g> -<!-- 23->12 --> -<g id="edge37" class="edge"> -<title>23->12</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1911.6,-359.7C1917.89,-351.39 1925.55,-341.28 1932.46,-332.14"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1935.3,-334.19 1938.55,-324.1 1929.72,-329.96 1935.3,-334.19"/> -</g> -<!-- 24->7 --> -<g id="edge26" class="edge"> -<title>24->7</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1094.58,-145.82C1097.6,-145.2 1100.58,-144.59 1103.5,-144 1183.8,-127.78 1206.36,-124.57 1290.09,-108.27"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1290.91,-111.67 1300.05,-106.32 1289.56,-104.8 1290.91,-111.67"/> -</g> -<!-- 24->8 --> -<g id="edge28" class="edge"> -<title>24->8</title> -<path fill="none" stroke="grey" stroke-width="2" d="M973.37,-143.97C944.46,-134.14 907.93,-121.73 877.5,-111.39"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="878.45,-108.01 867.85,-108.11 876.2,-114.64 878.45,-108.01"/> -</g> -<!-- 24->9 --> -<g id="edge30" class="edge"> -<title>24->9</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1018.56,-143.7C1016.33,-135.9 1013.65,-126.51 1011.17,-117.83"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1014.5,-116.76 1008.39,-108.1 1007.77,-118.68 1014.5,-116.76"/> -</g> -<!-- 24->10 --> -<g id="edge32" class="edge"> -<title>24->10</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1065.58,-143.88C1089.3,-134.22 1119.12,-122.09 1144.2,-111.88"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1145.62,-115.08 1153.56,-108.07 1142.98,-108.6 1145.62,-115.08"/> -</g> -<!-- 25->7 --> -<g id="edge27" class="edge"> -<title>25->7</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1224.41,-143.97C1252.5,-134.19 1287.96,-121.84 1317.57,-111.52"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1319.07,-114.71 1327.37,-108.11 1316.77,-108.09 1319.07,-114.71"/> -</g> -<!-- 25->8 --> -<g id="edge29" class="edge"> -<title>25->8</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1112.71,-145.98C1109.6,-145.3 1106.52,-144.63 1103.5,-144 1019.87,-126.46 996.21,-124.35 908.32,-108.14"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="908.92,-104.69 898.45,-106.31 907.64,-111.57 908.92,-104.69"/> -</g> -<!-- 25->9 --> -<g id="edge31" class="edge"> -<title>25->9</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1133.42,-143.88C1109.7,-134.22 1079.88,-122.09 1054.8,-111.88"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1056.02,-108.6 1045.44,-108.07 1053.38,-115.08 1056.02,-108.6"/> -</g> -<!-- 25->10 --> -<g id="edge33" class="edge"> -<title>25->10</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1180.44,-143.7C1182.67,-135.9 1185.35,-126.51 1187.83,-117.83"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.23,-118.68 1190.61,-108.1 1184.5,-116.76 1191.23,-118.68"/> +<!-- 32 --> +<g id="node33" class="node"><title>32</title> +<path fill="none" stroke="#b6d856" stroke-width="2" d="M1668,-324C1668,-324 1580,-324 1580,-324 1574,-324 1568,-318 1568,-312 1568,-312 1568,-300 1568,-300 1568,-294 1574,-288 1580,-288 1580,-288 1668,-288 1668,-288 1674,-288 1680,-294 1680,-300 1680,-300 1680,-312 1680,-312 1680,-318 1674,-324 1668,-324"/> +<text text-anchor="middle" x="1624" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text> 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1668.42,-331.45 1671.36,-325.099"/> +</g> +<!-- 25->12 --> +<g id="edge32" class="edge"><title>25->12</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-215.876C1472.55,-206.893 1488.13,-195.763 1501.75,-186.034"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-188.85 1509.93,-180.19 1499.76,-183.154 1503.83,-188.85"/> </g> -<!-- 26->13 --> -<g id="edge38" class="edge"> -<title>26->13</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1736.47,-215.7C1737.79,-207.98 1739.38,-198.71 1740.85,-190.11"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1744.33,-190.55 1742.57,-180.1 1737.43,-189.37 1744.33,-190.55"/> +<!-- 26 --> +<g id="node27" class="node"><title>26</title> +<path fill="none" stroke="#97d856" stroke-width="2" d="M1729,-252C1729,-252 1649,-252 1649,-252 1643,-252 1637,-246 1637,-240 1637,-240 1637,-228 1637,-228 1637,-222 1643,-216 1649,-216 1649,-216 1729,-216 1729,-216 1735,-216 1741,-222 1741,-228 1741,-228 1741,-240 1741,-240 1741,-246 1735,-252 1729,-252"/> +<text text-anchor="middle" x="1689" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text> </g> -<!-- 27 --> -<g id="node28" class="node"> -<title>27</title> -<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1928.5,-252C1928.5,-252 1836.5,-252 1836.5,-252 1830.5,-252 1824.5,-246 1824.5,-240 1824.5,-240 1824.5,-228 1824.5,-228 1824.5,-222 1830.5,-216 1836.5,-216 1836.5,-216 1928.5,-216 1928.5,-216 1934.5,-216 1940.5,-222 1940.5,-228 1940.5,-228 1940.5,-240 1940.5,-240 1940.5,-246 1934.5,-252 1928.5,-252"/> -<text text-anchor="middle" x="1882.5" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text> +<!-- 26->12 --> +<g id="edge33" class="edge"><title>26->12</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-215.876C1626.56,-204.799 1594.8,-190.457 1570.55,-179.504"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-176.264 1561.32,-175.338 1568.99,-182.643 1571.87,-176.264"/> +</g> +<!-- 26->13 --> +<g id="edge35" class="edge"><title>26->13</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-215.697C1681.83,-207.898 1679.15,-198.509 1676.67,-189.829"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-188.758 1673.89,-180.104 1673.27,-190.681 1680,-188.758"/> </g> <!-- 27->13 --> -<g id="edge39" class="edge"> -<title>27->13</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1848.99,-215.88C1828.65,-205.49 1802.7,-192.22 1781.87,-181.58"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1783.19,-178.33 1772.69,-176.9 1780.01,-184.56 1783.19,-178.33"/> -</g> -<!-- 27->14 --> -<g id="edge41" class="edge"> -<title>27->14</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1880.03,-215.7C1878.93,-207.98 1877.6,-198.71 1876.37,-190.11"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.82,-189.51 1874.94,-180.1 1872.89,-190.5 1879.82,-189.51"/> -</g> -<!-- 28->14 --> -<g id="edge40" class="edge"> -<title>28->14</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1992.6,-215.88C1967.01,-204.61 1933.73,-189.96 1908.7,-178.94"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1910.1,-175.73 1899.54,-174.9 1907.28,-182.14 1910.1,-175.73"/> +<g id="edge34" class="edge"><title>27->13</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-215.876C1761.56,-204.799 1729.8,-190.457 1705.55,-179.504"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-176.264 1696.32,-175.338 1703.99,-182.643 1706.87,-176.264"/> +</g> +<!-- 28 --> +<g id="node29" class="node"><title>28</title> +<path fill="none" stroke="#70d856" stroke-width="2" d="M994,-617C994,-617 726,-617 726,-617 720,-617 714,-611 714,-605 714,-605 714,-593 714,-593 714,-587 720,-581 726,-581 726,-581 994,-581 994,-581 1000,-581 1006,-587 1006,-593 1006,-593 1006,-605 1006,-605 1006,-611 1000,-617 994,-617"/> +<text text-anchor="middle" x="860" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> +<text text-anchor="middle" x="860" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text> +</g> +<!-- 28->15 --> +<g id="edge38" class="edge"><title>28->15</title> +<path fill="none" stroke="grey" stroke-width="2" d="M860,-580.819C860,-572.422 860,-562.116 860,-552.686"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-552.558 860,-542.558 856.5,-552.558 863.5,-552.558"/> </g> <!-- 29 --> -<g id="node30" class="node"> -<title>29</title> -<path fill="none" stroke="#70d856" stroke-width="2" d="M1062,-617C1062,-617 761,-617 761,-617 755,-617 749,-611 749,-605 749,-605 749,-593 749,-593 749,-587 755,-581 761,-581 761,-581 1062,-581 1062,-581 1068,-581 1074,-587 1074,-593 1074,-593 1074,-605 1074,-605 1074,-611 1068,-617 1062,-617"/> -<text text-anchor="middle" x="911.5" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> -<text text-anchor="middle" x="911.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text> +<g id="node30" class="node"><title>29</title> +<path fill="none" stroke="#d85656" stroke-width="2" d="M1056.5,-324C1056.5,-324 955.5,-324 955.5,-324 949.5,-324 943.5,-318 943.5,-312 943.5,-312 943.5,-300 943.5,-300 943.5,-294 949.5,-288 955.5,-288 955.5,-288 1056.5,-288 1056.5,-288 1062.5,-288 1068.5,-294 1068.5,-300 1068.5,-300 1068.5,-312 1068.5,-312 1068.5,-318 1062.5,-324 1056.5,-324"/> +<text text-anchor="middle" x="1006" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text> +<text text-anchor="middle" x="1006" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text> </g> <!-- 29->16 --> -<g id="edge44" class="edge"> -<title>29->16</title> -<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-580.82C911.5,-572.42 911.5,-562.12 911.5,-552.69"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="915,-552.56 911.5,-542.56 908,-552.56 915,-552.56"/> +<g id="edge39" class="edge"><title>29->16</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-287.697C1029.57,-279.22 1039.04,-268.864 1047.52,-259.583"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-261.846 1054.36,-252.104 1045.03,-257.123 1050.2,-261.846"/> </g> -<!-- 30 --> -<g id="node31" class="node"> -<title>30</title> -<path fill="none" stroke="#567bd8" stroke-width="2" d="M1128,-324C1128,-324 1013,-324 1013,-324 1007,-324 1001,-318 1001,-312 1001,-312 1001,-300 1001,-300 1001,-294 1007,-288 1013,-288 1013,-288 1128,-288 1128,-288 1134,-288 1140,-294 1140,-300 1140,-300 1140,-312 1140,-312 1140,-318 1134,-324 1128,-324"/> -<text text-anchor="middle" x="1070.5" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text> -<text text-anchor="middle" x="1070.5" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text> +<!-- 33 --> +<g id="node34" class="node"><title>33</title> +<path fill="none" stroke="#56d892" stroke-width="2" d="M985.5,-252C985.5,-252 900.5,-252 900.5,-252 894.5,-252 888.5,-246 888.5,-240 888.5,-240 888.5,-228 888.5,-228 888.5,-222 894.5,-216 900.5,-216 900.5,-216 985.5,-216 985.5,-216 991.5,-216 997.5,-222 997.5,-228 997.5,-228 997.5,-240 997.5,-240 997.5,-246 991.5,-252 985.5,-252"/> +<text text-anchor="middle" x="943" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text> +<text text-anchor="middle" x="943" y="-226" font-family="sans" font-size="10.00">kmer: 31</text> </g> -<!-- 30->17 --> -<g id="edge45" class="edge"> -<title>30->17</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1053.2,-287.7C1044.64,-279.14 1034.16,-268.66 1024.8,-259.3"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1027.15,-256.7 1017.6,-252.1 1022.2,-261.65 1027.15,-256.7"/> +<!-- 29->33 --> +<g id="edge62" class="edge"><title>29->33</title> +<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-287.697C982.798,-279.22 973.477,-268.864 965.124,-259.583"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-257.196 958.394,-252.104 962.482,-261.879 967.685,-257.196"/> </g> -<!-- 33 --> -<g id="node34" class="node"> -<title>33</title> -<path fill="none" stroke="#bed856" stroke-width="2" d="M1188,-252C1188,-252 1091,-252 1091,-252 1085,-252 1079,-246 1079,-240 1079,-240 1079,-228 1079,-228 1079,-222 1085,-216 1091,-216 1091,-216 1188,-216 1188,-216 1194,-216 1200,-222 1200,-228 1200,-228 1200,-240 1200,-240 1200,-246 1194,-252 1188,-252"/> -<text text-anchor="middle" x="1139.5" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text> -<text text-anchor="middle" x="1139.5" y="-226" font-family="sans" font-size="10.00">kmer: 31</text> -</g> -<!-- 30->33 --> -<g id="edge60" class="edge"> -<title>30->33</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1087.56,-287.7C1096,-279.14 1106.32,-268.66 1115.54,-259.3"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.11,-261.68 1122.64,-252.1 1113.13,-256.77 1118.11,-261.68"/> +<!-- 30 --> +<g id="node31" class="node"><title>30</title> +<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1330,-617C1330,-617 1050,-617 1050,-617 1044,-617 1038,-611 1038,-605 1038,-605 1038,-593 1038,-593 1038,-587 1044,-581 1050,-581 1050,-581 1330,-581 1330,-581 1336,-581 1342,-587 1342,-593 1342,-593 1342,-605 1342,-605 1342,-611 1336,-617 1330,-617"/> +<text text-anchor="middle" x="1190" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text> +<text text-anchor="middle" x="1190" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text> </g> -<!-- 31 --> -<g id="node32" class="node"> -<title>31</title> -<path fill="none" stroke="#56d89a" stroke-width="2" d="M1423,-617C1423,-617 1110,-617 1110,-617 1104,-617 1098,-611 1098,-605 1098,-605 1098,-593 1098,-593 1098,-587 1104,-581 1110,-581 1110,-581 1423,-581 1423,-581 1429,-581 1435,-587 1435,-593 1435,-593 1435,-605 1435,-605 1435,-611 1429,-617 1423,-617"/> -<text text-anchor="middle" x="1266.5" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text> -<text text-anchor="middle" x="1266.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text> +<!-- 30->17 --> +<g id="edge40" class="edge"><title>30->17</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1190,-580.819C1190,-572.422 1190,-562.116 1190,-552.686"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-552.558 1190,-542.558 1186.5,-552.558 1193.5,-552.558"/> </g> <!-- 31->18 --> -<g id="edge46" class="edge"> -<title>31->18</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-580.82C1266.5,-572.42 1266.5,-562.12 1266.5,-552.69"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1270,-552.56 1266.5,-542.56 1263,-552.56 1270,-552.56"/> -</g> -<!-- 32 --> -<g id="node33" class="node"> -<title>32</title> -<path fill="none" stroke="#566bd8" stroke-width="2" d="M1893,-545C1893,-545 1778,-545 1778,-545 1772,-545 1766,-539 1766,-533 1766,-533 1766,-516 1766,-516 1766,-510 1772,-504 1778,-504 1778,-504 1893,-504 1893,-504 1899,-504 1905,-510 1905,-516 1905,-516 1905,-533 1905,-533 1905,-539 1899,-545 1893,-545"/> -<text text-anchor="middle" x="1835.5" y="-533" font-family="sans" font-size="10.00">create_index_star</text> -<text text-anchor="middle" x="1835.5" y="-522" font-family="sans" font-size="10.00">index_size: 75</text> -<text text-anchor="middle" x="1835.5" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text> -</g> -<!-- 32->19 --> -<g id="edge47" class="edge"> -<title>32->19</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1765.88,-511.04C1692.65,-497.93 1577.92,-477.39 1503.47,-464.06"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.69,-460.55 1493.23,-462.23 1502.46,-467.44 1503.69,-460.55"/> -</g> -<!-- 32->22 --> -<g id="edge50" class="edge"> -<title>32->22</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1835.5,-503.69C1835.5,-495.91 1835.5,-486.84 1835.5,-478.45"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1839,-478.32 1835.5,-468.32 1832,-478.32 1839,-478.32"/> -</g> -<!-- 32->27 --> -<g id="edge58" class="edge"> -<title>32->27</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1888.04,-503.93C1932.59,-484.19 1993.58,-448.99 2021.5,-396 2044.78,-351.82 2024.92,-324.18 1990.5,-288 1977.81,-274.66 1961.04,-264.22 1944.52,-256.27"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1945.95,-253.07 1935.4,-252.1 1943.04,-259.44 1945.95,-253.07"/> -</g> -<!-- 33->24 --> -<g id="edge54" class="edge"> -<title>33->24</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1111.12,-215.88C1095.96,-206.72 1077.09,-195.34 1060.76,-185.48"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1062.36,-182.36 1051.99,-180.19 1058.74,-188.35 1062.36,-182.36"/> -</g> -<!-- 33->25 --> -<g id="edge56" class="edge"> -<title>33->25</title> -<path fill="none" stroke="grey" stroke-width="2" d="M1148.4,-215.7C1152.5,-207.73 1157.45,-198.1 1161.99,-189.26"/> -<polygon fill="grey" stroke="grey" stroke-width="2" points="1165.24,-190.6 1166.7,-180.1 1159.02,-187.4 1165.24,-190.6"/> +<g id="edge41" class="edge"><title>31->18</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1498.99,-287.697C1510.81,-278.796 1525.39,-267.823 1538.18,-258.199"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-260.915 1546.28,-252.104 1536.18,-255.322 1540.39,-260.915"/> +</g> +<!-- 32->18 --> +<g id="edge42" class="edge"><title>32->18</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1610.4,-287.697C1603.88,-279.389 1595.93,-269.277 1588.75,-260.141"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-257.805 1582.44,-252.104 1585.87,-262.13 1591.37,-257.805"/> +</g> +<!-- 33->19 --> +<g id="edge44" class="edge"><title>33->19</title> +<path fill="none" stroke="grey" stroke-width="2" d="M938.303,-215.697C936.187,-207.898 933.638,-198.509 931.282,-189.829"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="934.64,-188.838 928.643,-180.104 927.884,-190.672 934.64,-188.838"/> +</g> +<!-- 33->20 --> +<g id="edge46" class="edge"><title>33->20</title> +<path fill="none" stroke="grey" stroke-width="2" d="M971.866,-215.876C987.295,-206.724 1006.48,-195.342 1023.1,-185.485"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-188.302 1032.02,-180.19 1021.64,-182.282 1025.21,-188.302"/> +</g> +<!-- 34 --> +<g id="node35" class="node"><title>34</title> +<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1767.5,-545C1767.5,-545 1666.5,-545 1666.5,-545 1660.5,-545 1654.5,-539 1654.5,-533 1654.5,-533 1654.5,-516 1654.5,-516 1654.5,-510 1660.5,-504 1666.5,-504 1666.5,-504 1767.5,-504 1767.5,-504 1773.5,-504 1779.5,-510 1779.5,-516 1779.5,-516 1779.5,-533 1779.5,-533 1779.5,-539 1773.5,-545 1767.5,-545"/> +<text text-anchor="middle" x="1717" y="-533" font-family="sans" font-size="10.00">create_index_star</text> +<text text-anchor="middle" x="1717" y="-522" font-family="sans" font-size="10.00">index_size: 75</text> +<text text-anchor="middle" x="1717" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text> +</g> +<!-- 34->21 --> +<g id="edge47" class="edge"><title>34->21</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1654.4,-511.365C1586.62,-498.225 1478.92,-477.349 1409.61,-463.913"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1410.16,-460.453 1399.67,-461.986 1408.82,-467.325 1410.16,-460.453"/> +</g> +<!-- 34->23 --> +<g id="edge50" class="edge"><title>34->23</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1717,-503.689C1717,-495.907 1717,-486.842 1717,-478.447"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1720.5,-478.319 1717,-468.319 1713.5,-478.32 1720.5,-478.319"/> +</g> +<!-- 34->26 --> +<g id="edge54" class="edge"><title>34->26</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1763.03,-503.97C1804.26,-483.684 1862.09,-447.634 1888,-396 1896.33,-379.398 1897.01,-302.975 1885,-288 1848.05,-241.922 1813.46,-265.709 1751.06,-252.017"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.78,-248.589 1741.23,-249.598 1750.11,-255.386 1751.78,-248.589"/> +</g> +<!-- 35 --> +<g id="node36" class="node"><title>35</title> +<path fill="none" stroke="#a7d856" stroke-width="2" d="M1619.5,-396C1619.5,-396 1498.5,-396 1498.5,-396 1492.5,-396 1486.5,-390 1486.5,-384 1486.5,-384 1486.5,-372 1486.5,-372 1486.5,-366 1492.5,-360 1498.5,-360 1498.5,-360 1619.5,-360 1619.5,-360 1625.5,-360 1631.5,-366 1631.5,-372 1631.5,-372 1631.5,-384 1631.5,-384 1631.5,-390 1625.5,-396 1619.5,-396"/> +<text text-anchor="middle" x="1559" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text> +</g> +<!-- 35->31 --> +<g id="edge58" class="edge"><title>35->31</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1538.48,-359.697C1528.13,-350.965 1515.41,-340.24 1504.16,-330.75"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1506.18,-327.876 1496.28,-324.104 1501.67,-333.227 1506.18,-327.876"/> +</g> +<!-- 35->32 --> +<g id="edge61" class="edge"><title>35->32</title> +<path fill="none" stroke="grey" stroke-width="2" d="M1575.07,-359.697C1582.94,-351.22 1592.56,-340.864 1601.17,-331.583"/> +<polygon fill="grey" stroke="grey" stroke-width="2" points="1603.88,-333.814 1608.12,-324.104 1598.75,-329.051 1603.88,-333.814"/> </g> </g> </svg> diff --git a/images/rule_graph.svg 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d="M596.5,-468C596.5,-468 509.5,-468 509.5,-468 503.5,-468 497.5,-462 497.5,-456 497.5,-456 497.5,-444 497.5,-444 497.5,-438 503.5,-432 509.5,-432 509.5,-432 596.5,-432 596.5,-432 602.5,-432 608.5,-438 608.5,-444 608.5,-444 608.5,-456 608.5,-456 608.5,-462 602.5,-468 596.5,-468"/> +<path fill="none" stroke="#56d8c9" stroke-width="2" d="M596.5,-468C596.5,-468 509.5,-468 509.5,-468 503.5,-468 497.5,-462 497.5,-456 497.5,-456 497.5,-444 497.5,-444 497.5,-438 503.5,-432 509.5,-432 509.5,-432 596.5,-432 596.5,-432 602.5,-432 608.5,-438 608.5,-444 608.5,-444 608.5,-456 608.5,-456 608.5,-462 602.5,-468 596.5,-468"/> <text text-anchor="middle" x="553" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text> </g> <!-- 13->16 --> -<g id="edge32" class="edge"><title>13->16</title> +<g id="edge33" class="edge"><title>13->16</title> <path fill="none" stroke="grey" stroke-width="2" d="M598.169,-503.697C590.975,-495.305 582.203,-485.07 574.31,-475.861"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-473.419 567.661,-468.104 571.511,-477.975 576.826,-473.419"/> </g> <!-- 19 --> <g id="node20" class="node"><title>19</title> -<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1002.5,-468C1002.5,-468 929.5,-468 929.5,-468 923.5,-468 917.5,-462 917.5,-456 917.5,-456 917.5,-444 917.5,-444 917.5,-438 923.5,-432 929.5,-432 929.5,-432 1002.5,-432 1002.5,-432 1008.5,-432 1014.5,-438 1014.5,-444 1014.5,-444 1014.5,-456 1014.5,-456 1014.5,-462 1008.5,-468 1002.5,-468"/> +<path fill="none" stroke="#56d892" stroke-width="2" d="M1002.5,-468C1002.5,-468 929.5,-468 929.5,-468 923.5,-468 917.5,-462 917.5,-456 917.5,-456 917.5,-444 917.5,-444 917.5,-438 923.5,-432 929.5,-432 929.5,-432 1002.5,-432 1002.5,-432 1008.5,-432 1014.5,-438 1014.5,-444 1014.5,-444 1014.5,-456 1014.5,-456 1014.5,-462 1008.5,-468 1002.5,-468"/> <text text-anchor="middle" x="966" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text> </g> <!-- 13->19 --> @@ -206,7 +206,7 @@ </g> <!-- 14 --> <g id="node15" class="node"><title>14</title> -<path fill="none" stroke="#d8ac56" stroke-width="2" d="M577,-252C577,-252 501,-252 501,-252 495,-252 489,-246 489,-240 489,-240 489,-228 489,-228 489,-222 495,-216 501,-216 501,-216 577,-216 577,-216 583,-216 589,-222 589,-228 589,-228 589,-240 589,-240 589,-246 583,-252 577,-252"/> +<path fill="none" stroke="#97d856" stroke-width="2" d="M577,-252C577,-252 501,-252 501,-252 495,-252 489,-246 489,-240 489,-240 489,-228 489,-228 489,-222 495,-216 501,-216 501,-216 577,-216 577,-216 583,-216 589,-222 589,-228 589,-228 589,-240 589,-240 589,-246 583,-252 577,-252"/> <text text-anchor="middle" x="539" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text> </g> <!-- 14->5 --> @@ -215,72 +215,72 @@ <polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-185.344 492.905,-180.104 496.836,-189.943 502.114,-185.344"/> </g> <!-- 15->6 --> -<g id="edge17" class="edge"><title>15->6</title> 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d="M926,-396C926,-396 776,-396 776,-396 770,-396 764,-390 764,-384 764,-384 764,-372 764,-372 764,-366 770,-360 776,-360 776,-360 926,-360 926,-360 932,-360 938,-366 938,-372 938,-372 938,-384 938,-384 938,-390 932,-396 926,-396"/> +<path fill="none" stroke="#ced856" stroke-width="2" d="M926,-396C926,-396 776,-396 776,-396 770,-396 764,-390 764,-384 764,-384 764,-372 764,-372 764,-366 770,-360 776,-360 776,-360 926,-360 926,-360 932,-360 938,-366 938,-372 938,-372 938,-384 938,-384 938,-390 932,-396 926,-396"/> <text text-anchor="middle" x="851" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text> </g> <!-- 17->18 --> -<g id="edge37" class="edge"><title>17->18</title> +<g id="edge36" class="edge"><title>17->18</title> <path fill="none" stroke="grey" stroke-width="2" d="M844.978,-431.697C845.859,-423.983 846.919,-414.712 847.901,-406.112"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-406.437 849.045,-396.104 844.432,-405.642 851.387,-406.437"/> </g> <!-- 25 --> <g id="node26" class="node"><title>25</title> -<path fill="none" stroke="#56d0d8" stroke-width="2" d="M780,-324C780,-324 692,-324 692,-324 686,-324 680,-318 680,-312 680,-312 680,-300 680,-300 680,-294 686,-288 692,-288 692,-288 780,-288 780,-288 786,-288 792,-294 792,-300 792,-300 792,-312 792,-312 792,-318 786,-324 780,-324"/> +<path fill="none" stroke="#56a2d8" stroke-width="2" d="M780,-324C780,-324 692,-324 692,-324 686,-324 680,-318 680,-312 680,-312 680,-300 680,-300 680,-294 686,-288 692,-288 692,-288 780,-288 780,-288 786,-288 792,-294 792,-300 792,-300 792,-312 792,-312 792,-318 786,-324 780,-324"/> <text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text> </g> <!-- 17->25 --> -<g id="edge45" class="edge"><title>17->25</title> +<g id="edge42" class="edge"><title>17->25</title> <path fill="none" stroke="grey" stroke-width="2" d="M799.53,-431.827C783.272,-423.345 766.08,-411.537 755,-396 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class="edge"><title>19->8</title> <path fill="none" stroke="grey" stroke-width="2" d="M970.876,-431.724C975.205,-412.573 978.916,-381.548 965,-360 948.17,-333.94 914.888,-320.48 888.609,-313.662"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-310.183 878.57,-311.284 887.494,-316.994 889.107,-310.183"/> </g> <!-- 19->18 --> -<g id="edge36" class="edge"><title>19->18</title> +<g id="edge37" class="edge"><title>19->18</title> <path fill="none" stroke="grey" stroke-width="2" d="M937.868,-431.876C922.832,-422.724 904.133,-411.342 887.94,-401.485"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-398.4 879.24,-396.19 885.962,-404.379 889.602,-398.4"/> </g> <!-- 19->25 --> -<g id="edge44" class="edge"><title>19->25</title> +<g id="edge45" class="edge"><title>19->25</title> <path fill="none" stroke="grey" stroke-width="2" d="M967.332,-431.807C967.882,-411.847 965.54,-379.215 947,-360 941.799,-354.609 861.991,-335.541 802.055,-321.821"/> <polygon 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class="node"><title>22</title> -<path fill="none" stroke="#80d856" stroke-width="2" d="M407,-612C407,-612 281,-612 281,-612 275,-612 269,-606 269,-600 269,-600 269,-588 269,-588 269,-582 275,-576 281,-576 281,-576 407,-576 407,-576 413,-576 419,-582 419,-588 419,-588 419,-600 419,-600 419,-606 413,-612 407,-612"/> +<path fill="none" stroke="#d8c356" stroke-width="2" d="M407,-612C407,-612 281,-612 281,-612 275,-612 269,-606 269,-600 269,-600 269,-588 269,-588 269,-582 275,-576 281,-576 281,-576 407,-576 407,-576 413,-576 419,-582 419,-588 419,-588 419,-600 419,-600 419,-606 413,-612 407,-612"/> <text text-anchor="middle" x="344" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> </g> <!-- 22->11 --> @@ -311,7 +311,7 @@ </g> <!-- 23 --> <g id="node24" class="node"><title>23</title> -<path fill="none" stroke="#56d8c9" stroke-width="2" d="M238.5,-612C238.5,-612 151.5,-612 151.5,-612 145.5,-612 139.5,-606 139.5,-600 139.5,-600 139.5,-588 139.5,-588 139.5,-582 145.5,-576 151.5,-576 151.5,-576 238.5,-576 238.5,-576 244.5,-576 250.5,-582 250.5,-588 250.5,-588 250.5,-600 250.5,-600 250.5,-606 244.5,-612 238.5,-612"/> +<path fill="none" stroke="#d88d56" stroke-width="2" d="M238.5,-612C238.5,-612 151.5,-612 151.5,-612 145.5,-612 139.5,-606 139.5,-600 139.5,-600 139.5,-588 139.5,-588 139.5,-582 145.5,-576 151.5,-576 151.5,-576 238.5,-576 238.5,-576 244.5,-576 250.5,-582 250.5,-588 250.5,-588 250.5,-600 250.5,-600 250.5,-606 244.5,-612 238.5,-612"/> <text text-anchor="middle" x="195" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text> </g> <!-- 23->12 --> @@ -321,7 +321,7 @@ </g> <!-- 26 --> <g id="node27" class="node"><title>26</title> -<path fill="none" stroke="#d89c56" stroke-width="2" d="M522.5,-540C522.5,-540 437.5,-540 437.5,-540 431.5,-540 425.5,-534 425.5,-528 425.5,-528 425.5,-516 425.5,-516 425.5,-510 431.5,-504 437.5,-504 437.5,-504 522.5,-504 522.5,-504 528.5,-504 534.5,-510 534.5,-516 534.5,-516 534.5,-528 534.5,-528 534.5,-534 528.5,-540 522.5,-540"/> +<path fill="none" stroke="#d86656" stroke-width="2" d="M522.5,-540C522.5,-540 437.5,-540 437.5,-540 431.5,-540 425.5,-534 425.5,-528 425.5,-528 425.5,-516 425.5,-516 425.5,-510 431.5,-504 437.5,-504 437.5,-504 522.5,-504 522.5,-504 528.5,-504 534.5,-510 534.5,-516 534.5,-516 534.5,-528 534.5,-528 534.5,-534 528.5,-540 522.5,-540"/> <text text-anchor="middle" x="480" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text> </g> <!-- 23->26 --> @@ -331,7 +331,7 @@ </g> <!-- 24 --> <g id="node25" class="node"><title>24</title> -<path fill="none" stroke="#56d873" stroke-width="2" d="M668,-612C668,-612 558,-612 558,-612 552,-612 546,-606 546,-600 546,-600 546,-588 546,-588 546,-582 552,-576 558,-576 558,-576 668,-576 668,-576 674,-576 680,-582 680,-588 680,-588 680,-600 680,-600 680,-606 674,-612 668,-612"/> +<path fill="none" stroke="#56d85b" stroke-width="2" d="M668,-612C668,-612 558,-612 558,-612 552,-612 546,-606 546,-600 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d="M498.045,-503.697C507.062,-495.05 518.118,-484.449 527.943,-475.027"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-477.552 535.163,-468.104 525.522,-472.499 530.367,-477.552"/> </g> <!-- 27 --> <g id="node28" class="node"><title>27</title> -<path fill="none" stroke="#d8c356" stroke-width="2" d="M1001,-540C1001,-540 931,-540 931,-540 925,-540 919,-534 919,-528 919,-528 919,-516 919,-516 919,-510 925,-504 931,-504 931,-504 1001,-504 1001,-504 1007,-504 1013,-510 1013,-516 1013,-516 1013,-528 1013,-528 1013,-534 1007,-540 1001,-540"/> +<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1001,-540C1001,-540 931,-540 931,-540 925,-540 919,-534 919,-528 919,-528 919,-516 919,-516 919,-510 925,-504 931,-504 931,-504 1001,-504 1001,-504 1007,-504 1013,-510 1013,-516 1013,-516 1013,-528 1013,-528 1013,-534 1007,-540 1001,-540"/> <text text-anchor="middle" x="966" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text> </g> <!-- 27->17 --> @@ -376,7 +376,7 @@ </g> <!-- 28 --> <g id="node29" class="node"><title>28</title> -<path fill="none" stroke="#56d85b" stroke-width="2" d="M695.5,-396C695.5,-396 574.5,-396 574.5,-396 568.5,-396 562.5,-390 562.5,-384 562.5,-384 562.5,-372 562.5,-372 562.5,-366 568.5,-360 574.5,-360 574.5,-360 695.5,-360 695.5,-360 701.5,-360 707.5,-366 707.5,-372 707.5,-372 707.5,-384 707.5,-384 707.5,-390 701.5,-396 695.5,-396"/> +<path fill="none" stroke="#b6d856" stroke-width="2" d="M695.5,-396C695.5,-396 574.5,-396 574.5,-396 568.5,-396 562.5,-390 562.5,-384 562.5,-384 562.5,-372 562.5,-372 562.5,-366 568.5,-360 574.5,-360 574.5,-360 695.5,-360 695.5,-360 701.5,-360 707.5,-366 707.5,-372 707.5,-372 707.5,-384 707.5,-384 707.5,-390 701.5,-396 695.5,-396"/> <text text-anchor="middle" x="635" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text> </g> <!-- 28->25 --> -- GitLab