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Handle polyA processing in input preparation script

Merged Handle polyA processing in input preparation script
input_features into master
Merged BIOPZ-Katsantoni Maria requested to merge input_features into master
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<!-- Title: snakemake_dag Pages: 1 -->
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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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<title>1&#45;&gt;0</title>
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<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 -->
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<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 -->
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<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="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>
<path fill="none" stroke="grey" stroke-width="2" d="M938.16,-215.95C898.46,-206.3 856.28,-193.49 841.5,-180 803.34,-145.17 821.8,-118.11 798.5,-72 793.86,-62.81 788.11,-53.14 782.73,-44.62"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1006.5,-108C1006.5,-108 908.5,-108 908.5,-108 902.5,-108 896.5,-102 896.5,-96 896.5,-96 896.5,-84 896.5,-84 896.5,-78 902.5,-72 908.5,-72 908.5,-72 1006.5,-72 1006.5,-72 1012.5,-72 1018.5,-78 1018.5,-84 1018.5,-84 1018.5,-96 1018.5,-96 1018.5,-102 1012.5,-108 1006.5,-108"/>
<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>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="803.32,-29.06 792.73,-28.93 800.93,-35.64 803.32,-29.06"/>
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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>
</g>
<!-- 8&#45;&gt;0 -->
<g id="edge8" class="edge">
<title>8&#45;&gt;0</title>
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<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>
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<text text-anchor="middle" x="1186.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 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>
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<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"/>
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<!-- 10&#45;&gt;4 -->
<g id="edge12" class="edge">
<title>10&#45;&gt;4</title>
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<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>
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<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>
</g>
<!-- 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="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>
</g>
<!-- 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="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>
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<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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<g id="edge20" class="edge">
<title>14&#45;&gt;8</title>
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<!-- 15 -->
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<title>15</title>
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<title>16</title>
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<text text-anchor="middle" x="684.5" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<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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<title>20&#45;&gt;18</title>
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<title>20&#45;&gt;19</title>
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