dag_test_workflow.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<!-- 0 -->
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<text text-anchor="middle" x="1035" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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<!-- 1 -->
<g id="node2" class="node"><title>1</title>
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<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 1&#45;&gt;0 -->
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<!-- 2 -->
<g id="node3" class="node"><title>2</title>
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<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 2&#45;&gt;0 -->
<g id="edge2" class="edge"><title>2&#45;&gt;0</title>
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<!-- 3 -->
<g id="node4" class="node"><title>3</title>
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<text text-anchor="middle" x="988" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 3&#45;&gt;0 -->
<g id="edge3" class="edge"><title>3&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M924.308,-161.332C821.372,-159.74 636.097,-146.808 700,-72 737.975,-27.5452 918.617,-20.167 997.736,-19.0937"/>
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<!-- 9 -->
<g id="node10" class="node"><title>9</title>
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<text text-anchor="middle" x="1286" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="1286" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 3&#45;&gt;9 -->
<g id="edge25" class="edge"><title>3&#45;&gt;9</title>
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<!-- 10 -->
<g id="node11" class="node"><title>10</title>
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<text text-anchor="middle" x="781" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="781" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 3&#45;&gt;10 -->
<g id="edge27" class="edge"><title>3&#45;&gt;10</title>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
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<text text-anchor="middle" x="949" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 3&#45;&gt;11 -->
<g id="edge29" class="edge"><title>3&#45;&gt;11</title>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="1122" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="1122" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 3&#45;&gt;12 -->
<g id="edge31" class="edge"><title>3&#45;&gt;12</title>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="1125" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
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<!-- 4&#45;&gt;0 -->
<g id="edge4" class="edge"><title>4&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1180.58,-158.69C1266.45,-153.149 1416.19,-134.476 1363,-72 1326.04,-28.5839 1150.54,-20.6164 1072.53,-19.2392"/>
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<!-- 4&#45;&gt;9 -->
<g id="edge26" class="edge"><title>4&#45;&gt;9</title>
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<!-- 4&#45;&gt;10 -->
<g id="edge28" class="edge"><title>4&#45;&gt;10</title>
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<!-- 4&#45;&gt;11 -->
<g id="edge30" class="edge"><title>4&#45;&gt;11</title>
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<!-- 4&#45;&gt;12 -->
<g id="edge32" class="edge"><title>4&#45;&gt;12</title>
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<!-- 5 -->
<g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="854" y="-234" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 5&#45;&gt;0 -->
<g id="edge5" class="edge"><title>5&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M810.971,-218.422C745.148,-189.906 632.065,-129.992 682,-72 722.482,-24.9863 915.576,-19.0926 997.796,-18.7562"/>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
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<text text-anchor="middle" x="1320" y="-234" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 6&#45;&gt;0 -->
<g id="edge6" class="edge"><title>6&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1336.81,-218.244C1366.11,-186.077 1419.98,-116.217 1382,-72 1342.39,-25.8749 1153.71,-19.4546 1072.41,-18.8661"/>
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<!-- 7 -->
<g id="node8" class="node"><title>7</title>
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<text text-anchor="middle" x="1504" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1504" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 7&#45;&gt;0 -->
<g id="edge7" class="edge"><title>7&#45;&gt;0</title>
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<!-- 8 -->
<g id="node9" class="node"><title>8</title>
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<text text-anchor="middle" x="1689" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1689" y="-82" font-family="sans" font-size="10.00">seqmode: single_end</text>
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<!-- 8&#45;&gt;0 -->
<g id="edge8" class="edge"><title>8&#45;&gt;0</title>
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<!-- 9&#45;&gt;0 -->
<g id="edge9" class="edge"><title>9&#45;&gt;0</title>
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<!-- 10&#45;&gt;0 -->
<g id="edge10" class="edge"><title>10&#45;&gt;0</title>
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<!-- 11&#45;&gt;0 -->
<g id="edge11" class="edge"><title>11&#45;&gt;0</title>
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<!-- 12&#45;&gt;0 -->
<g id="edge12" class="edge"><title>12&#45;&gt;0</title>
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<!-- 13 -->
<g id="node14" class="node"><title>13</title>
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<text text-anchor="middle" x="1003" y="-311" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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<!-- 13&#45;&gt;3 -->
<g id="edge13" class="edge"><title>13&#45;&gt;3</title>
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<!-- 13&#45;&gt;5 -->
<g id="edge17" class="edge"><title>13&#45;&gt;5</title>
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<!-- 22 -->
<g id="node23" class="node"><title>22</title>
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<text text-anchor="middle" x="1496" y="-234" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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<!-- 13&#45;&gt;22 -->
<g id="edge38" class="edge"><title>13&#45;&gt;22</title>
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<!-- 14 -->
<g id="node15" class="node"><title>14</title>
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<text text-anchor="middle" x="1103" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="1103" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="1103" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 14&#45;&gt;3 -->
<g id="edge14" class="edge"><title>14&#45;&gt;3</title>
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<!-- 14&#45;&gt;4 -->
<g id="edge16" class="edge"><title>14&#45;&gt;4</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1120.19,-190.905 1119.74,-180.319 1113.49,-188.872 1120.19,-190.905"/>
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<!-- 15 -->
<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="1320" y="-311" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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<!-- 15&#45;&gt;4 -->
<g id="edge15" class="edge"><title>15&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1292.2,-295.305C1275.56,-284.728 1254.18,-270.629 1236,-257 1205.95,-234.472 1173.35,-206.391 1151.3,-186.814"/>
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<!-- 15&#45;&gt;6 -->
<g id="edge19" class="edge"><title>15&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1320,-295.481C1320,-286.436 1320,-275.097 1320,-264.851"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1323.5,-264.711 1320,-254.711 1316.5,-264.711 1323.5,-264.711"/>
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<!-- 23 -->
<g id="node24" class="node"><title>23</title>
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<text text-anchor="middle" x="1619" y="-234" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 15&#45;&gt;23 -->
<g id="edge40" class="edge"><title>15&#45;&gt;23</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1380.11,-300.533C1427.04,-290.777 1494.01,-275.949 1560.49,-257.315"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1561.62,-260.631 1570.29,-254.538 1559.71,-253.896 1561.62,-260.631"/>
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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
<path fill="none" stroke="#d8b456" stroke-width="2" d="M904.5,-331.5C904.5,-331.5 803.5,-331.5 803.5,-331.5 797.5,-331.5 791.5,-325.5 791.5,-319.5 791.5,-319.5 791.5,-307.5 791.5,-307.5 791.5,-301.5 797.5,-295.5 803.5,-295.5 803.5,-295.5 904.5,-295.5 904.5,-295.5 910.5,-295.5 916.5,-301.5 916.5,-307.5 916.5,-307.5 916.5,-319.5 916.5,-319.5 916.5,-325.5 910.5,-331.5 904.5,-331.5"/>
<text text-anchor="middle" x="854" y="-316.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="854" y="-305.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 16&#45;&gt;5 -->
<g id="edge18" class="edge"><title>16&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M854,-295.481C854,-286.436 854,-275.097 854,-264.851"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="857.5,-264.711 854,-254.711 850.5,-264.711 857.5,-264.711"/>
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<!-- 16&#45;&gt;6 -->
<g id="edge20" class="edge"><title>16&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M914.759,-295.473C918.551,-294.588 922.321,-293.754 926,-293 955.541,-286.944 1128.09,-263.327 1234.82,-248.924"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1235.49,-252.365 1244.93,-247.56 1234.56,-245.428 1235.49,-252.365"/>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
<path fill="none" stroke="#56d86b" stroke-width="2" d="M1586,-180C1586,-180 1420,-180 1420,-180 1414,-180 1408,-174 1408,-168 1408,-168 1408,-156 1408,-156 1408,-150 1414,-144 1420,-144 1420,-144 1586,-144 1586,-144 1592,-144 1598,-150 1598,-156 1598,-156 1598,-168 1598,-168 1598,-174 1592,-180 1586,-180"/>
<text text-anchor="middle" x="1503" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 17&#45;&gt;7 -->
<g id="edge21" class="edge"><title>17&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1503.25,-143.697C1503.36,-135.983 1503.49,-126.712 1503.61,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1507.11,-118.153 1503.76,-108.104 1500.11,-118.053 1507.11,-118.153"/>
</g>
<!-- 18 -->
<g id="node19" class="node"><title>18</title>
<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1749.5,-180C1749.5,-180 1628.5,-180 1628.5,-180 1622.5,-180 1616.5,-174 1616.5,-168 1616.5,-168 1616.5,-156 1616.5,-156 1616.5,-150 1622.5,-144 1628.5,-144 1628.5,-144 1749.5,-144 1749.5,-144 1755.5,-144 1761.5,-150 1761.5,-156 1761.5,-156 1761.5,-168 1761.5,-168 1761.5,-174 1755.5,-180 1749.5,-180"/>
<text text-anchor="middle" x="1689" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 18&#45;&gt;7 -->
<g id="edge22" class="edge"><title>18&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1643.74,-143.876C1618,-134.137 1585.59,-121.872 1558.46,-111.608"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1559.7,-108.334 1549.11,-108.068 1557.22,-114.881 1559.7,-108.334"/>
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<!-- 18&#45;&gt;8 -->
<g id="edge24" class="edge"><title>18&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1689,-143.697C1689,-135.983 1689,-126.712 1689,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1692.5,-118.104 1689,-108.104 1685.5,-118.104 1692.5,-118.104"/>
</g>
<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<text text-anchor="middle" x="1867" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 19&#45;&gt;8 -->
<g id="edge23" class="edge"><title>19&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1823.46,-143.876C1798.8,-134.179 1767.78,-121.98 1741.75,-111.743"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1742.99,-108.471 1732.4,-108.068 1740.43,-114.985 1742.99,-108.471"/>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
<path fill="none" stroke="#5682d8" stroke-width="2" d="M1137,-406C1137,-406 869,-406 869,-406 863,-406 857,-400 857,-394 857,-394 857,-382 857,-382 857,-376 863,-370 869,-370 869,-370 1137,-370 1137,-370 1143,-370 1149,-376 1149,-382 1149,-382 1149,-394 1149,-394 1149,-400 1143,-406 1137,-406"/>
<text text-anchor="middle" x="1003" y="-391" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1003" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 20&#45;&gt;13 -->
<g id="edge33" class="edge"><title>20&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1003,-369.819C1003,-361.422 1003,-351.116 1003,-341.686"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1006.5,-341.558 1003,-331.558 999.5,-341.558 1006.5,-341.558"/>
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<!-- 21 -->
<g id="node22" class="node"><title>21</title>
<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1460,-406C1460,-406 1180,-406 1180,-406 1174,-406 1168,-400 1168,-394 1168,-394 1168,-382 1168,-382 1168,-376 1174,-370 1180,-370 1180,-370 1460,-370 1460,-370 1466,-370 1472,-376 1472,-382 1472,-382 1472,-394 1472,-394 1472,-400 1466,-406 1460,-406"/>
<text text-anchor="middle" x="1320" y="-391" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1320" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 21&#45;&gt;15 -->
<g id="edge34" class="edge"><title>21&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1320,-369.819C1320,-361.422 1320,-351.116 1320,-341.686"/>
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<!-- 22&#45;&gt;17 -->
<g id="edge35" class="edge"><title>22&#45;&gt;17</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.88,-190.348 1501.35,-180.058 1496.91,-189.675 1503.88,-190.348"/>
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<!-- 23&#45;&gt;19 -->
<g id="edge36" class="edge"><title>23&#45;&gt;19</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1800.2,-186.174 1808.82,-180.009 1798.24,-179.456 1800.2,-186.174"/>
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<!-- 24 -->
<g id="node25" class="node"><title>24</title>
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<text text-anchor="middle" x="1557" y="-322" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1557" y="-311" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1557" y="-300" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 24&#45;&gt;22 -->
<g id="edge37" class="edge"><title>24&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1540.97,-292.795C1533.47,-283.572 1524.45,-272.48 1516.46,-262.659"/>
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<!-- 24&#45;&gt;23 -->
<g id="edge39" class="edge"><title>24&#45;&gt;23</title>
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