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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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<!-- 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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<!-- 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>
<path fill="none" stroke="grey" stroke-width="2" d="M751.432,-215.849C741.551,-178.753 718.127,-90.8101 706.219,-46.1027"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="709.546,-44.9947 703.59,-36.2325 702.782,-46.7964 709.546,-44.9947"/>
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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>
<path fill="none" stroke="grey" stroke-width="2" d="M620.97,-290.41C590.929,-279.939 552.3,-266.475 520.644,-255.441"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="521.655,-252.087 511.061,-252.1 519.351,-258.697 521.655,-252.087"/>
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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>
<path fill="none" stroke="grey" stroke-width="2" d="M738.35,-290.717C742.959,-289.749 747.541,-288.832 752,-288 865.226,-266.87 898.018,-274.364 1015.13,-252.03"/>
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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>
<path fill="none" stroke="grey" stroke-width="2" d="M906.62,-290.63C902.698,-289.695 898.8,-288.808 895,-288 796.444,-267.04 767.467,-272.788 664.451,-251.962"/>
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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>
<path fill="none" stroke="grey" stroke-width="2" d="M1019.5,-143.876C993.62,-134.137 961.033,-121.872 933.759,-111.608"/>
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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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<!-- 16&#45;&gt;9 -->
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<g id="node18" class="node"><title>17</title>
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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 -->
<g id="edge22" class="edge"><title>17&#45;&gt;11</title>
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<g id="edge23" class="edge"><title>18&#45;&gt;13</title>
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<g id="node21" class="node"><title>20</title>
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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 -->
<g id="edge27" class="edge"><title>20&#45;&gt;19</title>
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