docs/workflow_kraken2.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<!-- 16 -->
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<title>16</title>
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<!-- 0&#45;&gt;16 -->
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<title>0&#45;&gt;16</title>
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<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
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<text text-anchor="middle" x="34.5" y="-447.5" font-family="sans" font-size="10.00">raw_report</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="115.5" y="-525" font-family="sans" font-size="10.00">prepare_short_reads</text>
<text text-anchor="middle" x="115.5" y="-514" font-family="sans" font-size="10.00">sample: bg1_ag1_s1</text>
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<!-- 2&#45;&gt;1 -->
<g id="edge3" class="edge">
<title>2&#45;&gt;1</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="64.15,-471.99 54.29,-468.1 59.57,-477.29 64.15,-471.99"/>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
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<!-- 2&#45;&gt;5 -->
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<title>2&#45;&gt;5</title>
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<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
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<text text-anchor="middle" x="121.5" y="-447.5" font-family="sans" font-size="10.00">raw_report</text>
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<!-- 3&#45;&gt;0 -->
<g id="edge2" class="edge">
<title>3&#45;&gt;0</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="88.16,-401.73 79.18,-396.1 82.7,-406.1 88.16,-401.73"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
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<text text-anchor="middle" x="289.5" y="-514" font-family="sans" font-size="10.00">sample: bg1_ag1_s2</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge4" class="edge">
<title>4&#45;&gt;3</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="166.8,-466.08 156.22,-465.47 164.1,-472.54 166.8,-466.08"/>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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<!-- 4&#45;&gt;6 -->
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<title>4&#45;&gt;6</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="318.45,-478.5 320.48,-468.1 312.41,-474.96 318.45,-478.5"/>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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<text text-anchor="middle" x="184.5" y="-375.5" font-family="sans" font-size="10.00">trimming_report</text>
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<!-- 5&#45;&gt;8 -->
<g id="edge9" class="edge">
<title>5&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M211.6,-431.7C207.5,-423.73 202.55,-414.1 198.01,-405.26"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="200.98,-403.4 193.3,-396.1 194.76,-406.6 200.98,-403.4"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
<path fill="none" stroke="#56d8d0" stroke-width="2" d="M448,-396C448,-396 377,-396 377,-396 371,-396 365,-390 365,-384 365,-384 365,-372 365,-372 365,-366 371,-360 377,-360 377,-360 448,-360 448,-360 454,-360 460,-366 460,-372 460,-372 460,-384 460,-384 460,-390 454,-396 448,-396"/>
<text text-anchor="middle" x="412.5" y="-375.5" font-family="sans" font-size="10.00">rmhost_bowtie2</text>
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<!-- 5&#45;&gt;10 -->
<g id="edge11" class="edge">
<title>5&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M266.98,-432.05C293.9,-422.24 327.98,-409.82 356.39,-399.46"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="357.59,-402.75 365.78,-396.03 355.19,-396.17 357.59,-402.75"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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<text text-anchor="middle" x="298.5" y="-375.5" font-family="sans" font-size="10.00">trimming_report</text>
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<!-- 6&#45;&gt;9 -->
<g id="edge10" class="edge">
<title>6&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M322.59,-431.7C318.95,-423.73 314.55,-414.1 310.51,-405.26"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="313.66,-403.74 306.32,-396.1 307.29,-406.65 313.66,-403.74"/>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
<path fill="none" stroke="#56d8d0" stroke-width="2" d="M561,-396C561,-396 490,-396 490,-396 484,-396 478,-390 478,-384 478,-384 478,-372 478,-372 478,-366 484,-360 490,-360 490,-360 561,-360 561,-360 567,-360 573,-366 573,-372 573,-372 573,-384 573,-384 573,-390 567,-396 561,-396"/>
<text text-anchor="middle" x="525.5" y="-375.5" font-family="sans" font-size="10.00">rmhost_bowtie2</text>
</g>
<!-- 6&#45;&gt;12 -->
<g id="edge13" class="edge">
<title>6&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M376.71,-432.41C404.13,-422.57 439.12,-410.01 468.28,-399.54"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="469.69,-402.75 477.92,-396.08 467.33,-396.16 469.69,-402.75"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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<text text-anchor="middle" x="190.5" y="-303.5" font-family="sans" font-size="10.00">trimming_report_merge</text>
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<!-- 7&#45;&gt;16 -->
<g id="edge20" class="edge">
<title>7&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M190.5,-287.87C190.5,-263.67 190.5,-219.21 190.5,-190.39"/>
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<!-- 8&#45;&gt;7 -->
<g id="edge7" class="edge">
<title>8&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M185.98,-359.7C186.64,-351.98 187.44,-342.71 188.18,-334.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="191.67,-334.37 189.03,-324.1 184.69,-333.77 191.67,-334.37"/>
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<!-- 9&#45;&gt;7 -->
<g id="edge8" class="edge">
<title>9&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M272.08,-359.88C258.09,-350.81 240.72,-339.55 225.61,-329.76"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="227.32,-326.69 217.02,-324.19 223.51,-332.57 227.32,-326.69"/>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
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<text text-anchor="middle" x="332.5" y="-303.5" font-family="sans" font-size="10.00">rmhost_report</text>
</g>
<!-- 10&#45;&gt;14 -->
<g id="edge17" class="edge">
<title>10&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M392.72,-359.7C382.75,-350.97 370.49,-340.24 359.64,-330.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="361.88,-328.06 352.05,-324.1 357.27,-333.32 361.88,-328.06"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
<path fill="none" stroke="#56d8d8" stroke-width="2" d="M451,-180C451,-180 374,-180 374,-180 368,-180 362,-174 362,-168 362,-168 362,-156 362,-156 362,-150 368,-144 374,-144 374,-144 451,-144 451,-144 457,-144 463,-150 463,-156 463,-156 463,-168 463,-168 463,-174 457,-180 451,-180"/>
<text text-anchor="middle" x="412.5" y="-159.5" font-family="sans" font-size="10.00">profiling_kraken2</text>
</g>
<!-- 10&#45;&gt;18 -->
<g id="edge23" class="edge">
<title>10&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M412.5,-359.85C412.5,-322.83 412.5,-235.18 412.5,-190.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="416,-190.23 412.5,-180.23 409,-190.23 416,-190.23"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
<path fill="none" stroke="#88d856" stroke-width="2" stroke-dasharray="5,2" d="M528.5,-468C528.5,-468 424.5,-468 424.5,-468 418.5,-468 412.5,-462 412.5,-456 412.5,-456 412.5,-444 412.5,-444 412.5,-438 418.5,-432 424.5,-432 424.5,-432 528.5,-432 528.5,-432 534.5,-432 540.5,-438 540.5,-444 540.5,-444 540.5,-456 540.5,-456 540.5,-462 534.5,-468 528.5,-468"/>
<text text-anchor="middle" x="476.5" y="-447.5" font-family="sans" font-size="10.00">rmhost_bowtie2_index</text>
</g>
<!-- 11&#45;&gt;10 -->
<g id="edge12" class="edge">
<title>11&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M460.68,-431.7C452.93,-423.22 443.46,-412.86 434.98,-403.58"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="437.47,-401.12 428.14,-396.1 432.3,-405.85 437.47,-401.12"/>
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<!-- 11&#45;&gt;12 -->
<g id="edge14" class="edge">
<title>11&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M488.61,-431.7C494.37,-423.47 501.36,-413.48 507.71,-404.42"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="510.66,-406.3 513.53,-396.1 504.92,-402.29 510.66,-406.3"/>
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<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
<path fill="none" stroke="#d8d356" stroke-width="2" d="M514.5,-324C514.5,-324 452.5,-324 452.5,-324 446.5,-324 440.5,-318 440.5,-312 440.5,-312 440.5,-300 440.5,-300 440.5,-294 446.5,-288 452.5,-288 452.5,-288 514.5,-288 514.5,-288 520.5,-288 526.5,-294 526.5,-300 526.5,-300 526.5,-312 526.5,-312 526.5,-318 520.5,-324 514.5,-324"/>
<text text-anchor="middle" x="483.5" y="-303.5" font-family="sans" font-size="10.00">rmhost_report</text>
</g>
<!-- 12&#45;&gt;15 -->
<g id="edge18" class="edge">
<title>12&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M515.12,-359.7C510.24,-351.56 504.31,-341.69 498.92,-332.7"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="501.91,-330.88 493.76,-324.1 495.91,-334.48 501.91,-330.88"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
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<text text-anchor="middle" x="554.5" y="-159.5" font-family="sans" font-size="10.00">profiling_kraken2</text>
</g>
<!-- 12&#45;&gt;19 -->
<g id="edge24" class="edge">
<title>12&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M529.04,-359.87C531.11,-349.51 533.66,-336.03 535.5,-324 542.66,-277.26 548.6,-222.52 551.85,-190.42"/>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
<path fill="none" stroke="#56d8a2" stroke-width="2" d="M372.5,-252C372.5,-252 274.5,-252 274.5,-252 268.5,-252 262.5,-246 262.5,-240 262.5,-240 262.5,-228 262.5,-228 262.5,-222 268.5,-216 274.5,-216 274.5,-216 372.5,-216 372.5,-216 378.5,-216 384.5,-222 384.5,-228 384.5,-228 384.5,-240 384.5,-240 384.5,-246 378.5,-252 372.5,-252"/>
<text text-anchor="middle" x="323.5" y="-231.5" font-family="sans" font-size="10.00">rmhost_report_merge</text>
</g>
<!-- 13&#45;&gt;16 -->
<g id="edge21" class="edge">
<title>13&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M290.96,-215.88C273.25,-206.55 251.15,-194.92 232.18,-184.94"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="233.64,-181.75 223.16,-180.19 230.38,-187.94 233.64,-181.75"/>
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<!-- 14&#45;&gt;13 -->
<g id="edge15" class="edge">
<title>14&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M330.28,-287.7C329.28,-279.98 328.09,-270.71 326.99,-262.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="330.45,-261.58 325.7,-252.1 323.5,-262.47 330.45,-261.58"/>
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<!-- 15&#45;&gt;13 -->
<g id="edge16" class="edge">
<title>15&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M444.36,-287.88C422.49,-278.31 395.04,-266.3 371.84,-256.15"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="373.08,-252.87 362.51,-252.07 370.27,-259.28 373.08,-252.87"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
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<text text-anchor="middle" x="127.5" y="-87.5" font-family="sans" font-size="10.00">qcreport_plot</text>
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<!-- 16&#45;&gt;17 -->
<g id="edge22" class="edge">
<title>16&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M174.93,-143.7C167.3,-135.22 157.98,-124.86 149.62,-115.58"/>
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<!-- 23 -->
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<title>23</title>
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