docs/dag.svg

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<text text-anchor="middle" x="315.12" y="-343" font-family="sans" font-size="10.00">database: gencode</text>
<text text-anchor="middle" x="315.12" y="-332" font-family="sans" font-size="10.00">genome: GRCh38</text>
<text text-anchor="middle" x="315.12" y="-321" font-family="sans" font-size="10.00">outdir: /datapool/reference_genomes</text>
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<title>9</title>
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<title>1&#45;&gt;11</title>
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<title>12</title>
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<title>1&#45;&gt;14</title>
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<title>2</title>
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<text text-anchor="middle" x="1066.12" y="-233" font-family="sans" font-size="10.00">database: gencode</text>
<text text-anchor="middle" x="1066.12" y="-222" font-family="sans" font-size="10.00">genome: GRCh38</text>
<text text-anchor="middle" x="1066.12" y="-211" font-family="sans" font-size="10.00">outdir: /datapool/reference_genomes</text>
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<title>2&#45;&gt;0</title>
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<title>13</title>
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<title>15</title>
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<text text-anchor="middle" x="1077.12" y="-101" font-family="sans" font-size="10.00">salmon_kmer_size: 31</text>
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<text text-anchor="middle" x="780.12" y="-332" font-family="sans" font-size="10.00">genome: GRCh38</text>
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<title>7</title>
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<title>7&#45;&gt;12</title>
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<title>7&#45;&gt;14</title>
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<!-- 8&#45;&gt;0 -->
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<title>8&#45;&gt;0</title>
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<!-- 9&#45;&gt;0 -->
<g id="edge8" class="edge">
<title>9&#45;&gt;0</title>
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<!-- 10&#45;&gt;0 -->
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<title>10&#45;&gt;0</title>
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<!-- 11&#45;&gt;0 -->
<g id="edge10" class="edge">
<title>11&#45;&gt;0</title>
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<title>12&#45;&gt;0</title>
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<!-- 13&#45;&gt;0 -->
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<title>13&#45;&gt;0</title>
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<!-- 14&#45;&gt;0 -->
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<title>14&#45;&gt;0</title>
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<!-- 15&#45;&gt;0 -->
<g id="edge14" class="edge">
<title>15&#45;&gt;0</title>
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<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
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<text text-anchor="middle" x="1671.12" y="-354" font-family="sans" font-size="10.00">get_genome</text>
<text text-anchor="middle" x="1671.12" y="-343" font-family="sans" font-size="10.00">database: gencode</text>
<text text-anchor="middle" x="1671.12" y="-332" font-family="sans" font-size="10.00">genome: GRCm39</text>
<text text-anchor="middle" x="1671.12" y="-321" font-family="sans" font-size="10.00">outdir: /datapool/reference_genomes</text>
<text text-anchor="middle" x="1671.12" y="-310" font-family="sans" font-size="10.00">release: M35</text>
<text text-anchor="middle" x="1671.12" y="-299" font-family="sans" font-size="10.00">species: mouse</text>
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<!-- 16&#45;&gt;0 -->
<g id="edge15" class="edge">
<title>16&#45;&gt;0</title>
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<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
<path fill="none" stroke="#56d8a9" stroke-width="2" stroke-dasharray="5,2" d="M1511.12,-237C1511.12,-237 1423.12,-237 1423.12,-237 1417.12,-237 1411.12,-231 1411.12,-225 1411.12,-225 1411.12,-213 1411.12,-213 1411.12,-207 1417.12,-201 1423.12,-201 1423.12,-201 1511.12,-201 1511.12,-201 1517.12,-201 1523.12,-207 1523.12,-213 1523.12,-213 1523.12,-225 1523.12,-225 1523.12,-231 1517.12,-237 1511.12,-237"/>
<text text-anchor="middle" x="1467.12" y="-216.5" font-family="sans" font-size="10.00">index_genome_fasta</text>
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<!-- 16&#45;&gt;21 -->
<g id="edge45" class="edge">
<title>16&#45;&gt;21</title>
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<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
<path fill="none" stroke="#88d856" stroke-width="2" stroke-dasharray="5,2" d="M1630.62,-237C1630.62,-237 1553.62,-237 1553.62,-237 1547.62,-237 1541.62,-231 1541.62,-225 1541.62,-225 1541.62,-213 1541.62,-213 1541.62,-207 1547.62,-201 1553.62,-201 1553.62,-201 1630.62,-201 1630.62,-201 1636.62,-201 1642.62,-207 1642.62,-213 1642.62,-213 1642.62,-225 1642.62,-225 1642.62,-231 1636.62,-237 1630.62,-237"/>
<text text-anchor="middle" x="1592.12" y="-216.5" font-family="sans" font-size="10.00">build_hisat2_index</text>
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<!-- 16&#45;&gt;24 -->
<g id="edge48" class="edge">
<title>16&#45;&gt;24</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1644.6,-291.74C1633.46,-276.51 1620.78,-259.17 1610.67,-245.35"/>
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<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
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<text text-anchor="middle" x="1648.12" y="-106.5" font-family="sans" font-size="10.00">build_cellranger_index</text>
</g>
<!-- 16&#45;&gt;25 -->
<g id="edge49" class="edge">
<title>16&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1667.27,-291.51C1662.68,-247.97 1655.1,-176.18 1650.99,-137.21"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1654.46,-136.72 1649.93,-127.14 1647.5,-137.45 1654.46,-136.72"/>
</g>
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
<path fill="none" stroke="#68d856" stroke-width="2" d="M1818.62,-127C1818.62,-127 1737.62,-127 1737.62,-127 1731.62,-127 1725.62,-121 1725.62,-115 1725.62,-115 1725.62,-103 1725.62,-103 1725.62,-97 1731.62,-91 1737.62,-91 1737.62,-91 1818.62,-91 1818.62,-91 1824.62,-91 1830.62,-97 1830.62,-103 1830.62,-103 1830.62,-115 1830.62,-115 1830.62,-121 1824.62,-127 1818.62,-127"/>
<text text-anchor="middle" x="1778.12" y="-112" font-family="sans" font-size="10.00">build_star_index</text>
<text text-anchor="middle" x="1778.12" y="-101" font-family="sans" font-size="10.00">sjdbOverhang: 100</text>
</g>
<!-- 16&#45;&gt;26 -->
<g id="edge51" class="edge">
<title>16&#45;&gt;26</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1689.03,-291.51C1710.59,-247.6 1746.24,-174.95 1765.25,-136.22"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1768.45,-137.66 1769.71,-127.14 1762.16,-134.57 1768.45,-137.66"/>
</g>
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
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<text text-anchor="middle" x="1901.12" y="-112" font-family="sans" font-size="10.00">build_star_index</text>
<text text-anchor="middle" x="1901.12" y="-101" font-family="sans" font-size="10.00">sjdbOverhang: 149</text>
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<!-- 16&#45;&gt;27 -->
<g id="edge53" class="edge">
<title>16&#45;&gt;27</title>
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<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
<path fill="none" stroke="#56d8d0" stroke-width="2" d="M2095.62,-127C2095.62,-127 2022.62,-127 2022.62,-127 2016.62,-127 2010.62,-121 2010.62,-115 2010.62,-115 2010.62,-103 2010.62,-103 2010.62,-97 2016.62,-91 2022.62,-91 2022.62,-91 2095.62,-91 2095.62,-91 2101.62,-91 2107.62,-97 2107.62,-103 2107.62,-103 2107.62,-115 2107.62,-115 2107.62,-121 2101.62,-127 2095.62,-127"/>
<text text-anchor="middle" x="2059.12" y="-106.5" font-family="sans" font-size="10.00">build_rsem_index</text>
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<!-- 16&#45;&gt;29 -->
<g id="edge56" class="edge">
<title>16&#45;&gt;29</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1767.17,-318.5C1855.05,-307.93 1976.62,-288.01 2012.12,-256 2045.88,-225.56 2055.52,-170.8 2058.19,-137.69"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
<path fill="none" stroke="#d85656" stroke-width="2" stroke-dasharray="5,2" d="M2506.12,-256C2506.12,-256 2338.12,-256 2338.12,-256 2332.12,-256 2326.12,-250 2326.12,-244 2326.12,-244 2326.12,-194 2326.12,-194 2326.12,-188 2332.12,-182 2338.12,-182 2338.12,-182 2506.12,-182 2506.12,-182 2512.12,-182 2518.12,-188 2518.12,-194 2518.12,-194 2518.12,-244 2518.12,-244 2518.12,-250 2512.12,-256 2506.12,-256"/>
<text text-anchor="middle" x="2422.12" y="-244" font-family="sans" font-size="10.00">get_transcript</text>
<text text-anchor="middle" x="2422.12" y="-233" font-family="sans" font-size="10.00">database: gencode</text>
<text text-anchor="middle" x="2422.12" y="-222" font-family="sans" font-size="10.00">genome: GRCm39</text>
<text text-anchor="middle" x="2422.12" y="-211" font-family="sans" font-size="10.00">outdir: /datapool/reference_genomes</text>
<text text-anchor="middle" x="2422.12" y="-200" font-family="sans" font-size="10.00">release: M35</text>
<text text-anchor="middle" x="2422.12" y="-189" font-family="sans" font-size="10.00">species: mouse</text>
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<!-- 17&#45;&gt;0 -->
<g id="edge16" class="edge">
<title>17&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M2325.89,-184.92C2282.6,-169.46 2239.32,-152.94 2231.12,-146 2202.09,-121.42 2220.5,-91.96 2188.12,-72 2116.01,-27.55 1508.11,-20.33 1349.73,-19.2"/>
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<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
<path fill="none" stroke="#56d86b" stroke-width="2" stroke-dasharray="5,2" d="M2344.12,-127C2344.12,-127 2252.12,-127 2252.12,-127 2246.12,-127 2240.12,-121 2240.12,-115 2240.12,-115 2240.12,-103 2240.12,-103 2240.12,-97 2246.12,-91 2252.12,-91 2252.12,-91 2344.12,-91 2344.12,-91 2350.12,-91 2356.12,-97 2356.12,-103 2356.12,-103 2356.12,-115 2356.12,-115 2356.12,-121 2350.12,-127 2344.12,-127"/>
<text text-anchor="middle" x="2298.12" y="-112" font-family="sans" font-size="10.00">build_kallisto_index</text>
<text text-anchor="middle" x="2298.12" y="-101" font-family="sans" font-size="10.00">kallisto_kmer_size: 31</text>
</g>
<!-- 17&#45;&gt;28 -->
<g id="edge55" class="edge">
<title>17&#45;&gt;28</title>
<path fill="none" stroke="grey" stroke-width="2" d="M2380.49,-181.74C2362.51,-166.08 2341.97,-148.19 2325.9,-134.19"/>
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<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
<path fill="none" stroke="#afd856" stroke-width="2" stroke-dasharray="5,2" d="M2480.12,-127C2480.12,-127 2386.12,-127 2386.12,-127 2380.12,-127 2374.12,-121 2374.12,-115 2374.12,-115 2374.12,-103 2374.12,-103 2374.12,-97 2380.12,-91 2386.12,-91 2386.12,-91 2480.12,-91 2480.12,-91 2486.12,-91 2492.12,-97 2492.12,-103 2492.12,-103 2492.12,-115 2492.12,-115 2492.12,-121 2486.12,-127 2480.12,-127"/>
<text text-anchor="middle" x="2433.12" y="-112" font-family="sans" font-size="10.00">build_salmon_index</text>
<text text-anchor="middle" x="2433.12" y="-101" font-family="sans" font-size="10.00">salmon_kmer_size: 31</text>
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<!-- 17&#45;&gt;30 -->
<g id="edge58" class="edge">
<title>17&#45;&gt;30</title>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
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<text text-anchor="middle" x="2136.12" y="-354" font-family="sans" font-size="10.00">get_annotation_gtf</text>
<text text-anchor="middle" x="2136.12" y="-343" font-family="sans" font-size="10.00">database: gencode</text>
<text text-anchor="middle" x="2136.12" y="-332" font-family="sans" font-size="10.00">genome: GRCm39</text>
<text text-anchor="middle" x="2136.12" y="-321" font-family="sans" font-size="10.00">outdir: /datapool/reference_genomes</text>
<text text-anchor="middle" x="2136.12" y="-310" font-family="sans" font-size="10.00">release: M35</text>
<text text-anchor="middle" x="2136.12" y="-299" font-family="sans" font-size="10.00">species: mouse</text>
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<!-- 18&#45;&gt;0 -->
<g id="edge17" class="edge">
<title>18&#45;&gt;0</title>
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<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
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<!-- 18&#45;&gt;22 -->
<g id="edge46" class="edge">
<title>18&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M2072.92,-291.89C2044.06,-275.39 2010.81,-256.39 1985.74,-242.07"/>
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<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
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<text text-anchor="middle" x="2236.12" y="-216.5" font-family="sans" font-size="10.00">convert_gtf_to_bed_format</text>
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<!-- 18&#45;&gt;23 -->
<g id="edge47" class="edge">
<title>18&#45;&gt;23</title>
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<!-- 19 -->
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<text text-anchor="middle" x="2606.12" y="-123" font-family="sans" font-size="10.00">database: gencode</text>
<text text-anchor="middle" x="2606.12" y="-112" font-family="sans" font-size="10.00">genome: GRCm39</text>
<text text-anchor="middle" x="2606.12" y="-101" font-family="sans" font-size="10.00">outdir: /datapool/reference_genomes</text>
<text text-anchor="middle" x="2606.12" y="-90" font-family="sans" font-size="10.00">release: M35</text>
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