dag_test_workflow.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
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<text text-anchor="middle" x="765.5" 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="162.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="162.5" 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="511.5" y="-93" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="511.5" 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="497.5" y="-231.5" 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="M529.12,-215.95C568.61,-193.87 637.19,-152.87 688.5,-108 710.51,-88.76 731.97,-63.22 746.62,-44.44"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
<path fill="none" stroke="#d8a456" stroke-width="2" d="M700,-252C700,-252 599,-252 599,-252 593,-252 587,-246 587,-240 587,-240 587,-228 587,-228 587,-222 593,-216 599,-216 599,-216 700,-216 700,-216 706,-216 712,-222 712,-228 712,-228 712,-240 712,-240 712,-246 706,-252 700,-252"/>
<text text-anchor="middle" x="649.5" y="-231.5" 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="M682.26,-215.99C696.54,-207.05 712.3,-194.85 722.5,-180 750.73,-138.9 760.44,-80.17 763.77,-46.17"/>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
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<text text-anchor="middle" x="823.5" y="-231.5" 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="M818.57,-215.83C815.61,-205.47 811.8,-191.99 808.5,-180 795.61,-133.13 781.12,-78.44 772.68,-46.38"/>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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<text text-anchor="middle" x="1020.5" y="-231.5" 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>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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<text text-anchor="middle" x="957.5" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="957.5" 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>
<path fill="none" stroke="grey" stroke-width="2" d="M910.53,-71.88C877.17,-59.71 833.02,-43.62 802.23,-32.39"/>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1210.5,-108C1210.5,-108 1114.5,-108 1114.5,-108 1108.5,-108 1102.5,-102 1102.5,-96 1102.5,-96 1102.5,-84 1102.5,-84 1102.5,-78 1108.5,-72 1114.5,-72 1114.5,-72 1210.5,-72 1210.5,-72 1216.5,-72 1222.5,-78 1222.5,-84 1222.5,-84 1222.5,-96 1222.5,-96 1222.5,-102 1216.5,-108 1210.5,-108"/>
<text text-anchor="middle" x="1162.5" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1162.5" 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>
<path fill="none" stroke="grey" stroke-width="2" d="M1102.2,-78.37C1019.06,-63.71 871.68,-37.72 802.86,-25.59"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="803.35,-22.12 792.9,-23.83 802.14,-29.01 803.35,-22.12"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
<path fill="none" stroke="#56d8a2" stroke-width="2" d="M755.5,-326.5C755.5,-326.5 627.5,-326.5 627.5,-326.5 621.5,-326.5 615.5,-320.5 615.5,-314.5 615.5,-314.5 615.5,-302.5 615.5,-302.5 615.5,-296.5 621.5,-290.5 627.5,-290.5 627.5,-290.5 755.5,-290.5 755.5,-290.5 761.5,-290.5 767.5,-296.5 767.5,-302.5 767.5,-302.5 767.5,-314.5 767.5,-314.5 767.5,-320.5 761.5,-326.5 755.5,-326.5"/>
<text text-anchor="middle" x="691.5" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 9&#45;&gt;3 -->
<g id="edge9" class="edge">
<title>9&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M645.52,-290.32C617.74,-279.94 582.15,-266.63 552.83,-255.68"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="553.74,-252.28 543.15,-252.06 551.29,-258.84 553.74,-252.28"/>
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<!-- 9&#45;&gt;5 -->
<g id="edge13" class="edge">
<title>9&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M722.78,-290.32C740.95,-280.34 764.02,-267.67 783.49,-256.97"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="785.36,-259.94 792.44,-252.06 781.99,-253.8 785.36,-259.94"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
<path fill="none" stroke="#88d856" stroke-width="2" d="M1237,-252C1237,-252 1136,-252 1136,-252 1130,-252 1124,-246 1124,-240 1124,-240 1124,-228 1124,-228 1124,-222 1130,-216 1136,-216 1136,-216 1237,-216 1237,-216 1243,-216 1249,-222 1249,-228 1249,-228 1249,-240 1249,-240 1249,-246 1243,-252 1237,-252"/>
<text text-anchor="middle" x="1186.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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<!-- 9&#45;&gt;18 -->
<g id="edge26" class="edge">
<title>9&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M767.61,-291.23C773.99,-290.06 780.35,-288.97 786.5,-288 928.12,-265.74 968.19,-276.39 1113.57,-252.03"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
<path fill="none" stroke="#56d88a" stroke-width="2" d="M565,-329C565,-329 450,-329 450,-329 444,-329 438,-323 438,-317 438,-317 438,-300 438,-300 438,-294 444,-288 450,-288 450,-288 565,-288 565,-288 571,-288 577,-294 577,-300 577,-300 577,-317 577,-317 577,-323 571,-329 565,-329"/>
<text text-anchor="middle" x="507.5" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="507.5" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="507.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 10&#45;&gt;3 -->
<g id="edge10" class="edge">
<title>10&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M504.77,-287.69C503.69,-279.91 502.44,-270.84 501.29,-262.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="504.72,-261.75 499.89,-252.32 497.79,-262.7 504.72,-261.75"/>
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<!-- 10&#45;&gt;4 -->
<g id="edge12" class="edge">
<title>10&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M545.93,-287.88C564.79,-278.25 587.57,-266.62 606.95,-256.72"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="608.56,-259.83 615.88,-252.17 605.38,-253.6 608.56,-259.83"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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<text text-anchor="middle" x="1025.5" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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<!-- 11&#45;&gt;4 -->
<g id="edge11" class="edge">
<title>11&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M958.46,-291.13C953.41,-290.03 948.38,-288.97 943.5,-288 848.22,-269.01 820.7,-271.51 722.24,-252.27"/>
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<!-- 11&#45;&gt;6 -->
<g id="edge15" class="edge">
<title>11&#45;&gt;6</title>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
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<text text-anchor="middle" x="1320.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
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<!-- 11&#45;&gt;19 -->
<g id="edge28" class="edge">
<title>11&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1092.69,-292.13C1136.95,-281.86 1196.4,-267.78 1257.02,-252.34"/>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
<path fill="none" stroke="#d6d856" stroke-width="2" d="M923,-326.5C923,-326.5 808,-326.5 808,-326.5 802,-326.5 796,-320.5 796,-314.5 796,-314.5 796,-302.5 796,-302.5 796,-296.5 802,-290.5 808,-290.5 808,-290.5 923,-290.5 923,-290.5 929,-290.5 935,-296.5 935,-302.5 935,-302.5 935,-314.5 935,-314.5 935,-320.5 929,-326.5 923,-326.5"/>
<text text-anchor="middle" x="865.5" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="865.5" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 12&#45;&gt;5 -->
<g id="edge14" class="edge">
<title>12&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M855.55,-290.32C850.47,-281.56 844.2,-270.73 838.55,-260.97"/>
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<!-- 12&#45;&gt;6 -->
<g id="edge16" class="edge">
<title>12&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M902.23,-290.32C923.95,-280.16 951.64,-267.21 974.76,-256.39"/>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
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<text text-anchor="middle" x="957.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
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<!-- 13&#45;&gt;7 -->
<g id="edge17" class="edge">
<title>13&#45;&gt;7</title>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1230.5,-180C1230.5,-180 1094.5,-180 1094.5,-180 1088.5,-180 1082.5,-174 1082.5,-168 1082.5,-168 1082.5,-156 1082.5,-156 1082.5,-150 1088.5,-144 1094.5,-144 1094.5,-144 1230.5,-144 1230.5,-144 1236.5,-144 1242.5,-150 1242.5,-156 1242.5,-156 1242.5,-168 1242.5,-168 1242.5,-174 1236.5,-180 1230.5,-180"/>
<text text-anchor="middle" x="1162.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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<!-- 14&#45;&gt;7 -->
<g id="edge18" class="edge">
<title>14&#45;&gt;7</title>
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<!-- 14&#45;&gt;8 -->
<g id="edge20" class="edge">
<title>14&#45;&gt;8</title>
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<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
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<text text-anchor="middle" x="1358.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
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<!-- 15&#45;&gt;8 -->
<g id="edge19" class="edge">
<title>15&#45;&gt;8</title>
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<title>16</title>
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<text text-anchor="middle" x="684.5" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<title>16&#45;&gt;9</title>
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<title>17</title>
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<text text-anchor="middle" x="1033.5" 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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<title>17&#45;&gt;11</title>
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<title>18&#45;&gt;13</title>
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<title>19&#45;&gt;15</title>
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<title>20</title>
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<text text-anchor="middle" x="1253.5" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1253.5" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1253.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<g id="edge25" class="edge">
<title>20&#45;&gt;18</title>
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<title>20&#45;&gt;19</title>
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