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="699" 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="462" 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>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="599" 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>
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<!-- 5 -->
<g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="756" 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>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
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<text text-anchor="middle" x="932" 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="879" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="879" 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="1065" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1065" 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 -->
<g id="node10" class="node"><title>9</title>
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<text text-anchor="middle" x="670" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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<!-- 9&#45;&gt;3 -->
<g id="edge9" class="edge"><title>9&#45;&gt;3</title>
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<!-- 9&#45;&gt;5 -->
<g id="edge13" class="edge"><title>9&#45;&gt;5</title>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
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<text text-anchor="middle" x="1082" 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>
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<!-- 10 -->
<g id="node11" class="node"><title>10</title>
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<text text-anchor="middle" x="491" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="491" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="491" 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>
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<!-- 10&#45;&gt;4 -->
<g id="edge12" class="edge"><title>10&#45;&gt;4</title>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
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<text text-anchor="middle" x="967" 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>
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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="1205" 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>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="823" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="823" 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>
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<!-- 12&#45;&gt;6 -->
<g id="edge16" class="edge"><title>12&#45;&gt;6</title>
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<!-- 13 -->
<g id="node14" class="node"><title>13</title>
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<text text-anchor="middle" x="879" 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>
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<text text-anchor="middle" x="1065" 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="1243" 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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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
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<text text-anchor="middle" x="657" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="657" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<text text-anchor="middle" x="973" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="973" 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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<!-- 17&#45;&gt;11 -->
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<text text-anchor="middle" x="1143" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1143" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1143" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 20&#45;&gt;18 -->
<g id="edge25" class="edge"><title>20&#45;&gt;18</title>
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<!-- 20&#45;&gt;19 -->
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