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 -->
<g id="edge1" class="edge"><title>1&#45;&gt;0</title>
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<!-- 2 -->
<g id="node3" class="node"><title>2</title>
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<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="642" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 3&#45;&gt;0 -->
<g id="edge3" class="edge"><title>3&#45;&gt;0</title>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="818" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 4&#45;&gt;0 -->
<g id="edge4" class="edge"><title>4&#45;&gt;0</title>
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<!-- 5 -->
<g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="1428" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
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<!-- 5&#45;&gt;0 -->
<g id="edge5" class="edge"><title>5&#45;&gt;0</title>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
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<text text-anchor="middle" x="1632" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
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<!-- 6&#45;&gt;0 -->
<g id="edge6" class="edge"><title>6&#45;&gt;0</title>
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<!-- 7 -->
<g id="node8" class="node"><title>7</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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<!-- 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="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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<!-- 8&#45;&gt;0 -->
<g id="edge8" class="edge"><title>8&#45;&gt;0</title>
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<!-- 9 -->
<g id="node10" class="node"><title>9</title>
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<text text-anchor="middle" x="949" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="949" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 9&#45;&gt;0 -->
<g id="edge9" class="edge"><title>9&#45;&gt;0</title>
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<!-- 10 -->
<g id="node11" class="node"><title>10</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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<!-- 10&#45;&gt;0 -->
<g id="edge10" class="edge"><title>10&#45;&gt;0</title>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
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<text text-anchor="middle" x="1530" y="-87.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 11&#45;&gt;0 -->
<g id="edge11" class="edge"><title>11&#45;&gt;0</title>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="1747" y="-87.5" font-family="sans" font-size="10.00">star_rpm</text>
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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="854" y="-306" 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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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
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<text text-anchor="middle" x="1315" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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<!-- 13&#45;&gt;16 -->
<g id="edge39" class="edge"><title>13&#45;&gt;16</title>
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<!-- 21 -->
<g id="node22" class="node"><title>21</title>
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<text text-anchor="middle" x="976" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 13&#45;&gt;21 -->
<g id="edge44" class="edge"><title>13&#45;&gt;21</title>
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<!-- 14 -->
<g id="node15" class="node"><title>14</title>
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<text text-anchor="middle" x="812" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</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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<!-- 15 -->
<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="1154" y="-306" 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="M1093.95,-291.497C1036.84,-276.202 958.661,-255.033 952,-252 913.239,-234.354 873.108,-206.15 846.993,-186.228"/>
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<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<text text-anchor="middle" x="1632" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
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<!-- 15&#45;&gt;19 -->
<g id="edge42" class="edge"><title>15&#45;&gt;19</title>
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<!-- 22 -->
<g id="node23" class="node"><title>22</title>
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<!-- 15&#45;&gt;22 -->
<g id="edge46" class="edge"><title>15&#45;&gt;22</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1125.61,-188.864 1119.62,-180.121 1118.85,-190.688 1125.61,-188.864"/>
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<!-- 16&#45;&gt;5 -->
<g id="edge17" class="edge"><title>16&#45;&gt;5</title>
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<!-- 16&#45;&gt;11 -->
<g id="edge31" class="edge"><title>16&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1350.89,-215.807C1369.48,-206.262 1392.16,-193.588 1411,-180 1430.13,-166.199 1431.44,-158.561 1450,-144 1463.79,-133.184 1479.75,-122.31 1493.77,-113.251"/>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1390,-180C1390,-180 1240,-180 1240,-180 1234,-180 1228,-174 1228,-168 1228,-168 1228,-156 1228,-156 1228,-150 1234,-144 1240,-144 1240,-144 1390,-144 1390,-144 1396,-144 1402,-150 1402,-156 1402,-156 1402,-168 1402,-168 1402,-174 1396,-180 1390,-180"/>
<text text-anchor="middle" x="1315" y="-165" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="1315" y="-154" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 16&#45;&gt;17 -->
<g id="edge40" class="edge"><title>16&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1315,-215.697C1315,-207.983 1315,-198.712 1315,-190.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1318.5,-190.104 1315,-180.104 1311.5,-190.104 1318.5,-190.104"/>
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<!-- 17&#45;&gt;5 -->
<g id="edge18" class="edge"><title>17&#45;&gt;5</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1393.59,-116.431 1400.25,-108.19 1389.91,-110.481 1393.59,-116.431"/>
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<!-- 17&#45;&gt;11 -->
<g id="edge32" class="edge"><title>17&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1380.41,-143.913C1414.38,-134.442 1456.34,-121.802 1493,-108 1493.1,-107.964 1493.19,-107.928 1493.29,-107.892"/>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
<path fill="none" stroke="#d6d856" stroke-width="2" d="M1591.5,-180C1591.5,-180 1470.5,-180 1470.5,-180 1464.5,-180 1458.5,-174 1458.5,-168 1458.5,-168 1458.5,-156 1458.5,-156 1458.5,-150 1464.5,-144 1470.5,-144 1470.5,-144 1591.5,-144 1591.5,-144 1597.5,-144 1603.5,-150 1603.5,-156 1603.5,-156 1603.5,-168 1603.5,-168 1603.5,-174 1597.5,-180 1591.5,-180"/>
<text text-anchor="middle" x="1531" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 18&#45;&gt;5 -->
<g id="edge19" class="edge"><title>18&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1505.8,-143.876C1492.59,-134.893 1476.21,-123.763 1461.89,-114.034"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1463.53,-110.916 1453.29,-108.19 1459.6,-116.705 1463.53,-110.916"/>
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<!-- 18&#45;&gt;6 -->
<g id="edge22" class="edge"><title>18&#45;&gt;6</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1600.97,-116.763 1607.2,-108.19 1596.98,-111.009 1600.97,-116.763"/>
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<!-- 19&#45;&gt;6 -->
<g id="edge20" class="edge"><title>19&#45;&gt;6</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1635.5,-118.189 1632,-108.189 1628.5,-118.189 1635.5,-118.189"/>
</g>
<!-- 19&#45;&gt;12 -->
<g id="edge33" class="edge"><title>19&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1680.75,-227.646C1736.69,-220.381 1823.26,-205.316 1843,-180 1852.84,-167.383 1851.13,-157.779 1843,-144 1830.39,-122.628 1805.73,-109.279 1784.56,-101.324"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1785.42,-97.9183 1774.83,-97.9398 1783.12,-104.53 1785.42,-97.9183"/>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1822,-180C1822,-180 1672,-180 1672,-180 1666,-180 1660,-174 1660,-168 1660,-168 1660,-156 1660,-156 1660,-150 1666,-144 1672,-144 1672,-144 1822,-144 1822,-144 1828,-144 1834,-150 1834,-156 1834,-156 1834,-168 1834,-168 1834,-174 1828,-180 1822,-180"/>
<text text-anchor="middle" x="1747" y="-165" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="1747" y="-154" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g>
<!-- 19&#45;&gt;20 -->
<g id="edge43" class="edge"><title>19&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1660.13,-215.876C1675.17,-206.724 1693.87,-195.342 1710.06,-185.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1712.04,-188.379 1718.76,-180.19 1708.4,-182.4 1712.04,-188.379"/>
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<!-- 20&#45;&gt;6 -->
<g id="edge21" class="edge"><title>20&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1718.87,-143.876C1703.83,-134.724 1685.13,-123.342 1668.94,-113.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1670.6,-110.4 1660.24,-108.19 1666.96,-116.379 1670.6,-110.4"/>
</g>
<!-- 20&#45;&gt;12 -->
<g id="edge34" class="edge"><title>20&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1747,-143.697C1747,-135.983 1747,-126.712 1747,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1750.5,-118.104 1747,-108.104 1743.5,-118.104 1750.5,-118.104"/>
</g>
<!-- 21&#45;&gt;7 -->
<g id="edge23" class="edge"><title>21&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1039.83,-146.527C1043.61,-145.672 1047.35,-144.824 1051,-144 1103.35,-132.163 1162.27,-118.875 1208.02,-108.565"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1208.88,-111.958 1217.87,-106.345 1207.34,-105.13 1208.88,-111.958"/>
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<!-- 21&#45;&gt;8 -->
<g id="edge25" class="edge"><title>21&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M928.298,-143.876C901.048,-134.094 866.703,-121.765 838.034,-111.474"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="839.142,-108.153 828.547,-108.068 836.777,-114.741 839.142,-108.153"/>
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<!-- 21&#45;&gt;9 -->
<g id="edge27" class="edge"><title>21&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M969.326,-143.697C966.285,-135.813 962.617,-126.304 959.239,-117.546"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="962.462,-116.175 955.597,-108.104 955.931,-118.694 962.462,-116.175"/>
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<!-- 21&#45;&gt;10 -->
<g id="edge29" class="edge"><title>21&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1011.72,-143.876C1031.5,-134.392 1056.27,-122.513 1077.33,-112.419"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1078.9,-115.548 1086.4,-108.068 1075.87,-109.236 1078.9,-115.548"/>
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<!-- 22&#45;&gt;7 -->
<g id="edge24" class="edge"><title>22&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1156.83,-143.876C1180.42,-134.222 1210.06,-122.087 1235,-111.878"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1236.38,-115.096 1244.3,-108.068 1233.72,-108.618 1236.38,-115.096"/>
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<!-- 22&#45;&gt;8 -->
<g id="edge26" class="edge"><title>22&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1059.24,-146.384C1055.78,-145.556 1052.35,-144.754 1049,-144 969.907,-126.177 947.224,-124.641 863.791,-108.136"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="864.358,-104.68 853.867,-106.159 862.991,-111.545 864.358,-104.68"/>
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<!-- 22&#45;&gt;9 -->
<g id="edge28" class="edge"><title>22&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1074.39,-143.876C1051.6,-134.264 1022.97,-122.193 998.83,-112.013"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1000.05,-108.729 989.476,-108.068 997.331,-115.179 1000.05,-108.729"/>
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<!-- 22&#45;&gt;10 -->
<g id="edge30" class="edge"><title>22&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1116.73,-143.697C1117.5,-135.983 1118.43,-126.712 1119.29,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1122.78,-118.403 1120.29,-108.104 1115.81,-117.706 1122.78,-118.403"/>
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<!-- 23 -->
<g id="node24" class="node"><title>23</title>
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<text text-anchor="middle" x="841" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="841" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 23&#45;&gt;13 -->
<g id="edge35" class="edge"><title>23&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M844.081,-364.819C845.586,-356.422 847.434,-346.116 849.125,-336.686"/>
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<!-- 24 -->
<g id="node25" class="node"><title>24</title>
<path fill="none" stroke="#61d856" stroke-width="2" d="M1057.5,-326.5C1057.5,-326.5 956.5,-326.5 956.5,-326.5 950.5,-326.5 944.5,-320.5 944.5,-314.5 944.5,-314.5 944.5,-302.5 944.5,-302.5 944.5,-296.5 950.5,-290.5 956.5,-290.5 956.5,-290.5 1057.5,-290.5 1057.5,-290.5 1063.5,-290.5 1069.5,-296.5 1069.5,-302.5 1069.5,-302.5 1069.5,-314.5 1069.5,-314.5 1069.5,-320.5 1063.5,-326.5 1057.5,-326.5"/>
<text text-anchor="middle" x="1007" y="-311.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
<text text-anchor="middle" x="1007" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 24&#45;&gt;14 -->
<g id="edge36" class="edge"><title>24&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M960.788,-290.319C932.86,-279.935 897.084,-266.634 867.613,-255.677"/>
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<!-- 27 -->
<g id="node28" class="node"><title>27</title>
<path fill="none" stroke="#566bd8" stroke-width="2" d="M1057.5,-252C1057.5,-252 972.5,-252 972.5,-252 966.5,-252 960.5,-246 960.5,-240 960.5,-240 960.5,-228 960.5,-228 960.5,-222 966.5,-216 972.5,-216 972.5,-216 1057.5,-216 1057.5,-216 1063.5,-216 1069.5,-222 1069.5,-228 1069.5,-228 1069.5,-240 1069.5,-240 1069.5,-246 1063.5,-252 1057.5,-252"/>
<text text-anchor="middle" x="1015" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="1015" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
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<!-- 24&#45;&gt;27 -->
<g id="edge48" class="edge"><title>24&#45;&gt;27</title>
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<!-- 25 -->
<g id="node26" class="node"><title>25</title>
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<text text-anchor="middle" x="1157" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1157" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 25&#45;&gt;15 -->
<g id="edge37" class="edge"><title>25&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1156.29,-364.819C1155.94,-356.422 1155.52,-346.116 1155.12,-336.686"/>
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<!-- 26 -->
<g id="node27" class="node"><title>26</title>
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<text text-anchor="middle" x="1473" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1473" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1473" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 26&#45;&gt;16 -->
<g id="edge38" class="edge"><title>26&#45;&gt;16</title>
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<!-- 26&#45;&gt;19 -->
<g id="edge41" class="edge"><title>26&#45;&gt;19</title>
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<!-- 27&#45;&gt;21 -->
<g id="edge45" class="edge"><title>27&#45;&gt;21</title>
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<!-- 27&#45;&gt;22 -->
<g id="edge47" class="edge"><title>27&#45;&gt;22</title>
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