diff --git a/README.md b/README.md
index eef5a21..12b3932 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,7 @@ _MIRFLOWZ_ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs.
 2. [Usage](#usage)
     - [Preparing inputs](#preparing-inputs)
     - [Running the workflow](#running-the-workflow)
+    - [Expected output files](#expected-output-files)
     - [Creating a Snakemake report](#creating-a-snakemake-report)
 3. [Workflow description](#workflow-description)
 4. [Contributing](#contributing)
@@ -219,7 +220,7 @@ We recommend creating a copy of the
 
 ```bash
 cp  config/config_template.yaml  path/to/config.yaml
-```
+``` So on that PR I could move this information in the section/file all of this will be written. 
 
 Open the new copy in your editor of choice and adjust the configuration
 parameters to your liking. The template explains what each of the
@@ -251,6 +252,49 @@ snakemake \
 After successful execution of the workflow, results and logs will be found in
 the `results/` and `logs/` directories, respectively.
 
+### Expected output files
+
+Upon successful execution of _MIRFLOWZ_, the tool automatically removes all
+intermediate files generated during the process. The final outputs comprise:
+
+1. A SAM file containing alignments intersecting a pri-miR locus. These
+alignments intersect with extended start and/or end positions specified in the
+provided pri-miR annotations. Please note that they may not contribute to the
+final counting and may not appear in the final table. Alignments are discarded
+if their start and/or end positions differ from the ends of the provided
+pri-miR annotations by more bases than the extension used.
+
+2. A SAM file containing alignments intersecting a mature miRNA locus. Similar
+to the previous file, these alignments intersect with extended start and/or end
+positions specified in the provided miRNA annotations. They may not contribute
+to the final counting and might be absent from the final table.
+
+3. A BAM file containing the set of alignments contributing to the final
+counting and its corresponding index file (`.bam.bai`).
+
+4. Table(s) containing the counting data from all libraries for (iso)miRs
+and/or pri-miRs. Each row corresponds to a miRNA species, and each column
+represents a sample library. Each read is counted towards all the annotated
+miRNA species it aligns to, with 1/n, where n is the number of genomic and/or
+transcriptomic loci that read aligns to.
+
+To retain all intermediate files, include `--no-hooks` in the workflow call.
+
+```bash
+snakemake \
+    --snakefile="path/to/Snakefile" \
+    --cores 4  \
+    --configfile="path/to/config.yaml" \
+    --use-conda \
+    --printshellcmds \
+    --rerun-incomplete \
+    --no-hooks \
+    --verbose
+```
+
+After successful execution of the workflow, the intermediate files will be
+found in the `results/intermediates` directory.
+
 ### Creating a Snakemake report
 
 Snakemake provides the option to generate a detailed HTML report on runtime
diff --git a/config/config_schema.json b/config/config_schema.json
index 2d56367..842c175 100644
--- a/config/config_schema.json
+++ b/config/config_schema.json
@@ -30,6 +30,11 @@
             "default": "results/",
             "description": "Path to the output directory."
         },
+        "intermediates_dir":{
+            "type": "string",
+            "default": "results/intermediates",
+            "description": "Path to the directory storing the intermediate files."
+        },
         "local_log":{
             "type": "string",
             "default": "logs/local/",
diff --git a/config/config_template.yaml b/config/config_template.yaml
index d6d01c9..06f89bd 100644
--- a/config/config_template.yaml
+++ b/config/config_template.yaml
@@ -32,6 +32,7 @@ map_chr_file: path/to/ucsc_ensembl_mappings.tsv
 #### DIRECTORIES ####
 
 output_dir: results/
+intermediates_dir: results/intermediates
 local_log: logs/local/
 cluster_log: logs/cluster/
 scripts_dir: ../scripts/
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 8926ad4..9836032 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
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-<text text-anchor="middle" x="498" y="-1959.5" font-family="sans" font-size="10.00">trim_genome_seq_id</text>
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+<text text-anchor="middle" x="453" y="-1959.5" font-family="sans" font-size="10.00">trim_genome_seq_ids</text>
 </g>
 <!-- 7&#45;&gt;6 -->
 <g id="edge14" class="edge">
 <title>7&#45;&gt;6</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="377.51,-1346.18 377.1,-1335.59 370.82,-1344.12 377.51,-1346.18"/>
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 <!-- 19 -->
 <g id="node20" class="node">
 <title>19</title>
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-<text text-anchor="middle" x="920" y="-1887.5" font-family="sans" font-size="10.00">extract_transcriptome_seqs</text>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M790.5,-1908C790.5,-1908 671.5,-1908 671.5,-1908 665.5,-1908 659.5,-1902 659.5,-1896 659.5,-1896 659.5,-1884 659.5,-1884 659.5,-1878 665.5,-1872 671.5,-1872 671.5,-1872 790.5,-1872 790.5,-1872 796.5,-1872 802.5,-1878 802.5,-1884 802.5,-1884 802.5,-1896 802.5,-1896 802.5,-1902 796.5,-1908 790.5,-1908"/>
+<text text-anchor="middle" x="731" y="-1887.5" font-family="sans" font-size="10.00">extract_transcriptome_seqs</text>
 </g>
 <!-- 7&#45;&gt;19 -->
 <g id="edge30" class="edge">
 <title>7&#45;&gt;19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M555.47,-1953.01C620.73,-1943.73 730.68,-1927.46 834.93,-1908.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="835.42,-1912.16 844.64,-1906.93 834.17,-1905.27 835.42,-1912.16"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M512.98,-1945.9C552.13,-1936.04 603.81,-1923.03 647.02,-1912.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="647.78,-1915.56 656.62,-1909.73 646.07,-1908.78 647.78,-1915.56"/>
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 <!-- 30 -->
 <g id="node31" class="node">
 <title>30</title>
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-<text text-anchor="middle" x="619" y="-1815.5" font-family="sans" font-size="10.00">map_genome_segemehl</text>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M565.5,-1836C565.5,-1836 458.5,-1836 458.5,-1836 452.5,-1836 446.5,-1830 446.5,-1824 446.5,-1824 446.5,-1812 446.5,-1812 446.5,-1806 452.5,-1800 458.5,-1800 458.5,-1800 565.5,-1800 565.5,-1800 571.5,-1800 577.5,-1806 577.5,-1812 577.5,-1812 577.5,-1824 577.5,-1824 577.5,-1830 571.5,-1836 565.5,-1836"/>
+<text text-anchor="middle" x="512" y="-1815.5" font-family="sans" font-size="10.00">map_genome_segemehl</text>
 </g>
 <!-- 7&#45;&gt;30 -->
 <g id="edge43" class="edge">
 <title>7&#45;&gt;30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M555.2,-1958.09C590.75,-1952.96 633.95,-1939.98 657,-1908 670.39,-1889.43 658.76,-1865.41 644.95,-1847.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="647.67,-1844.81 638.65,-1839.26 642.24,-1849.22 647.67,-1844.81"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M434.42,-1943.02C417.74,-1924.62 397.88,-1895.47 412,-1872 419.25,-1859.95 430.27,-1850.49 442.38,-1843.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="443.97,-1846.24 451.07,-1838.38 440.61,-1840.1 443.97,-1846.24"/>
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 <!-- 31 -->
 <g id="node32" class="node">
 <title>31</title>
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-<text text-anchor="middle" x="557" y="-1887.5" font-family="sans" font-size="10.00">generate_segemehl_index_genome</text>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M591,-1908C591,-1908 433,-1908 433,-1908 427,-1908 421,-1902 421,-1896 421,-1896 421,-1884 421,-1884 421,-1878 427,-1872 433,-1872 433,-1872 591,-1872 591,-1872 597,-1872 603,-1878 603,-1884 603,-1884 603,-1896 603,-1896 603,-1902 597,-1908 591,-1908"/>
+<text text-anchor="middle" x="512" y="-1887.5" font-family="sans" font-size="10.00">generate_segemehl_index_genome</text>
 </g>
 <!-- 7&#45;&gt;31 -->
-<g id="edge46" class="edge">
+<g id="edge45" class="edge">
 <title>7&#45;&gt;31</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="536.19,-1921.12 539.96,-1911.22 530.84,-1916.61 536.19,-1921.12"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M467.89,-1943.34C474.2,-1935.85 481.7,-1926.95 488.71,-1918.63"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="491.19,-1921.12 494.96,-1911.22 485.84,-1916.61 491.19,-1921.12"/>
 </g>
-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
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-<text text-anchor="middle" x="510" y="-1743.5" font-family="sans" font-size="10.00">map_genome_oligomap</text>
+<!-- 34 -->
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M683,-1764C683,-1764 579,-1764 579,-1764 573,-1764 567,-1758 567,-1752 567,-1752 567,-1740 567,-1740 567,-1734 573,-1728 579,-1728 579,-1728 683,-1728 683,-1728 689,-1728 695,-1734 695,-1740 695,-1740 695,-1752 695,-1752 695,-1758 689,-1764 683,-1764"/>
+<text text-anchor="middle" x="631" y="-1743.5" font-family="sans" font-size="10.00">map_genome_oligomap</text>
 </g>
-<!-- 7&#45;&gt;33 -->
+<!-- 7&#45;&gt;34 -->
 <g id="edge49" class="edge">
-<title>7&#45;&gt;33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M479.4,-1943.2C470.8,-1933.68 461.51,-1921.21 457,-1908 451.83,-1892.86 453.81,-1887.68 457,-1872 463.99,-1837.62 480.77,-1800.96 493.59,-1776.29"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="496.63,-1778.03 498.26,-1767.56 490.46,-1774.73 496.63,-1778.03"/>
+<title>7&#45;&gt;34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M512.89,-1956.51C547.18,-1950.65 588.03,-1937.45 612,-1908 641.96,-1871.2 640.7,-1813.03 636.34,-1777.6"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="639.82,-1777.2 634.94,-1767.8 632.89,-1778.2 639.82,-1777.2"/>
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 <!-- 41 -->
 <g id="node42" class="node">
 <title>41</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M392,-1260C392,-1260 270,-1260 270,-1260 264,-1260 258,-1254 258,-1248 258,-1248 258,-1236 258,-1236 258,-1230 264,-1224 270,-1224 270,-1224 392,-1224 392,-1224 398,-1224 404,-1230 404,-1236 404,-1236 404,-1248 404,-1248 404,-1254 398,-1260 392,-1260"/>
-<text text-anchor="middle" x="331" y="-1239.5" font-family="sans" font-size="10.00">create_index_genome_fasta</text>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M353,-1260C353,-1260 231,-1260 231,-1260 225,-1260 219,-1254 219,-1248 219,-1248 219,-1236 219,-1236 219,-1230 225,-1224 231,-1224 231,-1224 353,-1224 353,-1224 359,-1224 365,-1230 365,-1236 365,-1236 365,-1248 365,-1248 365,-1254 359,-1260 353,-1260"/>
+<text text-anchor="middle" x="292" y="-1239.5" font-family="sans" font-size="10.00">create_index_genome_fasta</text>
 </g>
 <!-- 7&#45;&gt;41 -->
-<g id="edge59" class="edge">
+<g id="edge57" class="edge">
 <title>7&#45;&gt;41</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="334.5,-1273.96 331,-1263.96 327.5,-1273.96 334.5,-1273.96"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M406,-1943.04C358.48,-1921.46 292,-1880.31 292,-1819 292,-1819 292,-1819 292,-1385 292,-1346.65 292,-1302.48 292,-1273.72"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="295.5,-1273.96 292,-1263.96 288.5,-1273.96 295.5,-1273.96"/>
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 <!-- 8 -->
 <g id="node9" class="node">
 <title>8</title>
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-<text text-anchor="middle" x="597" y="-1239.5" font-family="sans" font-size="10.00">merge_all_maps</text>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M591.5,-1260C591.5,-1260 524.5,-1260 524.5,-1260 518.5,-1260 512.5,-1254 512.5,-1248 512.5,-1248 512.5,-1236 512.5,-1236 512.5,-1230 518.5,-1224 524.5,-1224 524.5,-1224 591.5,-1224 591.5,-1224 597.5,-1224 603.5,-1230 603.5,-1236 603.5,-1236 603.5,-1248 603.5,-1248 603.5,-1254 597.5,-1260 591.5,-1260"/>
+<text text-anchor="middle" x="558" y="-1239.5" font-family="sans" font-size="10.00">merge_all_maps</text>
 </g>
 <!-- 8&#45;&gt;5 -->
-<g id="edge12" class="edge">
+<g id="edge13" class="edge">
 <title>8&#45;&gt;5</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="530.77,-1193.07 520.5,-1190.48 526.92,-1198.91 530.77,-1193.07"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M530.98,-1223.15C518.39,-1214.84 503.21,-1204.82 489.54,-1195.79"/>
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 <g id="node10" class="node">
 <title>9</title>
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-<text text-anchor="middle" x="792" y="-1311.5" font-family="sans" font-size="10.00">transcriptome_to_genome_maps</text>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M825.5,-1332C825.5,-1332 680.5,-1332 680.5,-1332 674.5,-1332 668.5,-1326 668.5,-1320 668.5,-1320 668.5,-1308 668.5,-1308 668.5,-1302 674.5,-1296 680.5,-1296 680.5,-1296 825.5,-1296 825.5,-1296 831.5,-1296 837.5,-1302 837.5,-1308 837.5,-1308 837.5,-1320 837.5,-1320 837.5,-1326 831.5,-1332 825.5,-1332"/>
+<text text-anchor="middle" x="753" y="-1311.5" font-family="sans" font-size="10.00">transcriptome_to_genome_maps</text>
 </g>
 <!-- 9&#45;&gt;8 -->
 <g id="edge16" class="edge">
 <title>9&#45;&gt;8</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="656.93,-1260.79 646.34,-1260.71 654.56,-1267.38 656.93,-1260.79"/>
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 <g id="node11" class="node">
 <title>10</title>
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-<text text-anchor="middle" x="925" y="-1383.5" font-family="sans" font-size="10.00">remove_header_transcriptome_mappings</text>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M962,-1404C962,-1404 776,-1404 776,-1404 770,-1404 764,-1398 764,-1392 764,-1392 764,-1380 764,-1380 764,-1374 770,-1368 776,-1368 776,-1368 962,-1368 962,-1368 968,-1368 974,-1374 974,-1380 974,-1380 974,-1392 974,-1392 974,-1398 968,-1404 962,-1404"/>
+<text text-anchor="middle" x="869" y="-1383.5" font-family="sans" font-size="10.00">remove_header_transcriptome_mappings</text>
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 <!-- 10&#45;&gt;9 -->
-<g id="edge17" class="edge">
+<g id="edge18" class="edge">
 <title>10&#45;&gt;9</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="839,-1335.78 828.52,-1334.22 835.74,-1341.98 839,-1335.78"/>
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 <g id="node12" class="node">
 <title>11</title>
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-<text text-anchor="middle" x="925" y="-1455.5" font-family="sans" font-size="10.00">filter_transcriptome_by_nh</text>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M927.5,-1476C927.5,-1476 810.5,-1476 810.5,-1476 804.5,-1476 798.5,-1470 798.5,-1464 798.5,-1464 798.5,-1452 798.5,-1452 798.5,-1446 804.5,-1440 810.5,-1440 810.5,-1440 927.5,-1440 927.5,-1440 933.5,-1440 939.5,-1446 939.5,-1452 939.5,-1452 939.5,-1464 939.5,-1464 939.5,-1470 933.5,-1476 927.5,-1476"/>
+<text text-anchor="middle" x="869" y="-1455.5" font-family="sans" font-size="10.00">filter_transcriptome_by_nh</text>
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 <!-- 11&#45;&gt;10 -->
 <g id="edge19" class="edge">
 <title>11&#45;&gt;10</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="928.5,-1417.93 925,-1407.93 921.5,-1417.93 928.5,-1417.93"/>
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 <g id="node13" class="node">
 <title>12</title>
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-<text text-anchor="middle" x="925" y="-1527.5" font-family="sans" font-size="10.00">merge_transcriptome_maps</text>
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 </g>
 <!-- 12&#45;&gt;11 -->
 <g id="edge20" class="edge">
 <title>12&#45;&gt;11</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="928.5,-1489.93 925,-1479.93 921.5,-1489.93 928.5,-1489.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M869,-1511.34C869,-1504.75 869,-1497.08 869,-1489.67"/>
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 <g id="node14" class="node">
 <title>13</title>
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-<text text-anchor="middle" x="1007" y="-1671.5" font-family="sans" font-size="10.00">map_transcriptome_segemehl</text>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1068.5,-1692C1068.5,-1692 935.5,-1692 935.5,-1692 929.5,-1692 923.5,-1686 923.5,-1680 923.5,-1680 923.5,-1668 923.5,-1668 923.5,-1662 929.5,-1656 935.5,-1656 935.5,-1656 1068.5,-1656 1068.5,-1656 1074.5,-1656 1080.5,-1662 1080.5,-1668 1080.5,-1668 1080.5,-1680 1080.5,-1680 1080.5,-1686 1074.5,-1692 1068.5,-1692"/>
+<text text-anchor="middle" x="1002" y="-1671.5" font-family="sans" font-size="10.00">map_transcriptome_segemehl</text>
 </g>
 <!-- 13&#45;&gt;12 -->
-<g id="edge22" class="edge">
+<g id="edge21" class="edge">
 <title>13&#45;&gt;12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M996.61,-1655.02C982.81,-1631.12 958.26,-1588.59 941.8,-1560.1"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="944.85,-1558.37 936.81,-1551.46 938.78,-1561.87 944.85,-1558.37"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M999.25,-1655.01C995.44,-1635.52 986.91,-1604.46 969,-1584 958.53,-1572.04 944.69,-1562.35 930.66,-1554.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="932.63,-1551.76 922.13,-1550.35 929.45,-1558 932.63,-1551.76"/>
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 <!-- 14 -->
 <g id="node15" class="node">
 <title>14</title>
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-<text text-anchor="middle" x="767" y="-1887.5" font-family="sans" font-size="10.00">collapse_identical_reads</text>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M935,-1908C935,-1908 833,-1908 833,-1908 827,-1908 821,-1902 821,-1896 821,-1896 821,-1884 821,-1884 821,-1878 827,-1872 833,-1872 833,-1872 935,-1872 935,-1872 941,-1872 947,-1878 947,-1884 947,-1884 947,-1896 947,-1896 947,-1902 941,-1908 935,-1908"/>
+<text text-anchor="middle" x="884" y="-1887.5" font-family="sans" font-size="10.00">collapse_identical_reads</text>
 </g>
 <!-- 14&#45;&gt;13 -->
-<g id="edge23" class="edge">
+<g id="edge25" class="edge">
 <title>14&#45;&gt;13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M830.96,-1873.81C880.71,-1861.73 945.44,-1845.35 971,-1836 1040.44,-1810.58 1081.62,-1826.59 1121,-1764 1129.52,-1750.46 1129.6,-1741.49 1121,-1728 1113.1,-1715.62 1101.48,-1706.08 1088.64,-1698.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1090.29,-1695.67 1079.8,-1694.24 1087.11,-1701.91 1090.29,-1695.67"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M947.79,-1877.92C1009.5,-1863.44 1099.71,-1831.48 1142,-1764 1150.5,-1750.44 1151.09,-1741.17 1142,-1728 1130.32,-1711.09 1112.49,-1699.57 1093.44,-1691.72"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1094.89,-1688.53 1084.29,-1688.34 1092.46,-1695.09 1094.89,-1688.53"/>
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-<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M823,-1836C823,-1836 715,-1836 715,-1836 709,-1836 703,-1830 703,-1824 703,-1824 703,-1812 703,-1812 703,-1806 709,-1800 715,-1800 715,-1800 823,-1800 823,-1800 829,-1800 835,-1806 835,-1812 835,-1812 835,-1824 835,-1824 835,-1830 829,-1836 823,-1836"/>
-<text text-anchor="middle" x="769" y="-1815.5" font-family="sans" font-size="10.00">filter_fasta_for_oligomap</text>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M793,-1836C793,-1836 685,-1836 685,-1836 679,-1836 673,-1830 673,-1824 673,-1824 673,-1812 673,-1812 673,-1806 679,-1800 685,-1800 685,-1800 793,-1800 793,-1800 799,-1800 805,-1806 805,-1812 805,-1812 805,-1824 805,-1824 805,-1830 799,-1836 793,-1836"/>
+<text text-anchor="middle" x="739" y="-1815.5" font-family="sans" font-size="10.00">filter_fasta_for_oligomap</text>
 </g>
-<!-- 14&#45;&gt;23 -->
+<!-- 14&#45;&gt;24 -->
 <g id="edge36" class="edge">
-<title>14&#45;&gt;23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M767.5,-1871.34C767.69,-1864.75 767.91,-1857.08 768.12,-1849.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="771.61,-1850.02 768.4,-1839.93 764.62,-1849.82 771.61,-1850.02"/>
+<title>14&#45;&gt;24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M847.04,-1871.15C829.04,-1862.47 807.16,-1851.91 787.81,-1842.56"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="789.4,-1839.45 778.88,-1838.25 786.36,-1845.75 789.4,-1839.45"/>
 </g>
 <!-- 14&#45;&gt;30 -->
 <g id="edge44" class="edge">
 <title>14&#45;&gt;30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M729.27,-1871.15C710.81,-1862.43 688.36,-1851.81 668.54,-1842.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="670.19,-1839.34 659.65,-1838.23 667.2,-1845.67 670.19,-1839.34"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M820.05,-1873.7C817.33,-1873.11 814.64,-1872.54 812,-1872 737.28,-1856.59 651.52,-1841.72 590.89,-1831.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="591.76,-1828.27 581.33,-1830.1 590.62,-1835.18 591.76,-1828.27"/>
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 <!-- 15 -->
 <g id="node16" class="node">
 <title>15</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M804,-1980C804,-1980 730,-1980 730,-1980 724,-1980 718,-1974 718,-1968 718,-1968 718,-1956 718,-1956 718,-1950 724,-1944 730,-1944 730,-1944 804,-1944 804,-1944 810,-1944 816,-1950 816,-1956 816,-1956 816,-1968 816,-1968 816,-1974 810,-1980 804,-1980"/>
-<text text-anchor="middle" x="767" y="-1959.5" font-family="sans" font-size="10.00">remove_adapters</text>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M921,-1980C921,-1980 847,-1980 847,-1980 841,-1980 835,-1974 835,-1968 835,-1968 835,-1956 835,-1956 835,-1950 841,-1944 847,-1944 847,-1944 921,-1944 921,-1944 927,-1944 933,-1950 933,-1956 933,-1956 933,-1968 933,-1968 933,-1974 927,-1980 921,-1980"/>
+<text text-anchor="middle" x="884" y="-1959.5" font-family="sans" font-size="10.00">remove_adapters</text>
 </g>
 <!-- 15&#45;&gt;14 -->
 <g id="edge26" class="edge">
 <title>15&#45;&gt;14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M767,-1943.34C767,-1936.75 767,-1929.08 767,-1921.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="770.5,-1921.93 767,-1911.93 763.5,-1921.93 770.5,-1921.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M884,-1943.34C884,-1936.75 884,-1929.08 884,-1921.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="887.5,-1921.93 884,-1911.93 880.5,-1921.93 887.5,-1921.93"/>
 </g>
 <!-- 16 -->
 <g id="node17" class="node">
 <title>16</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M793,-2052C793,-2052 741,-2052 741,-2052 735,-2052 729,-2046 729,-2040 729,-2040 729,-2028 729,-2028 729,-2022 735,-2016 741,-2016 741,-2016 793,-2016 793,-2016 799,-2016 805,-2022 805,-2028 805,-2028 805,-2040 805,-2040 805,-2046 799,-2052 793,-2052"/>
-<text text-anchor="middle" x="767" y="-2031.5" font-family="sans" font-size="10.00">format_fasta</text>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M910,-2052C910,-2052 858,-2052 858,-2052 852,-2052 846,-2046 846,-2040 846,-2040 846,-2028 846,-2028 846,-2022 852,-2016 858,-2016 858,-2016 910,-2016 910,-2016 916,-2016 922,-2022 922,-2028 922,-2028 922,-2040 922,-2040 922,-2046 916,-2052 910,-2052"/>
+<text text-anchor="middle" x="884" y="-2031.5" font-family="sans" font-size="10.00">format_fasta</text>
 </g>
 <!-- 16&#45;&gt;15 -->
 <g id="edge27" class="edge">
 <title>16&#45;&gt;15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M767,-2015.34C767,-2008.75 767,-2001.08 767,-1993.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="770.5,-1993.93 767,-1983.93 763.5,-1993.93 770.5,-1993.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M884,-2015.34C884,-2008.75 884,-2001.08 884,-1993.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="887.5,-1993.93 884,-1983.93 880.5,-1993.93 887.5,-1993.93"/>
 </g>
 <!-- 17 -->
 <g id="node18" class="node">
 <title>17</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M782,-2124C782,-2124 752,-2124 752,-2124 746,-2124 740,-2118 740,-2112 740,-2112 740,-2100 740,-2100 740,-2094 746,-2088 752,-2088 752,-2088 782,-2088 782,-2088 788,-2088 794,-2094 794,-2100 794,-2100 794,-2112 794,-2112 794,-2118 788,-2124 782,-2124"/>
-<text text-anchor="middle" x="767" y="-2103.5" font-family="sans" font-size="10.00">start</text>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M899,-2124C899,-2124 869,-2124 869,-2124 863,-2124 857,-2118 857,-2112 857,-2112 857,-2100 857,-2100 857,-2094 863,-2088 869,-2088 869,-2088 899,-2088 899,-2088 905,-2088 911,-2094 911,-2100 911,-2100 911,-2112 911,-2112 911,-2118 905,-2124 899,-2124"/>
+<text text-anchor="middle" x="884" y="-2103.5" font-family="sans" font-size="10.00">start</text>
 </g>
 <!-- 17&#45;&gt;16 -->
 <g id="edge28" class="edge">
 <title>17&#45;&gt;16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M767,-2087.34C767,-2080.75 767,-2073.08 767,-2065.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="770.5,-2065.93 767,-2055.93 763.5,-2065.93 770.5,-2065.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M884,-2087.34C884,-2080.75 884,-2073.08 884,-2065.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="887.5,-2065.93 884,-2055.93 880.5,-2065.93 887.5,-2065.93"/>
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 <!-- 18 -->
 <g id="node19" class="node">
 <title>18</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M949.5,-1836C949.5,-1836 872.5,-1836 872.5,-1836 866.5,-1836 860.5,-1830 860.5,-1824 860.5,-1824 860.5,-1812 860.5,-1812 860.5,-1806 866.5,-1800 872.5,-1800 872.5,-1800 949.5,-1800 949.5,-1800 955.5,-1800 961.5,-1806 961.5,-1812 961.5,-1812 961.5,-1824 961.5,-1824 961.5,-1830 955.5,-1836 949.5,-1836"/>
-<text text-anchor="middle" x="911" y="-1815.5" font-family="sans" font-size="10.00">trim_fasta_seq_ids</text>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M955,-1836C955,-1836 835,-1836 835,-1836 829,-1836 823,-1830 823,-1824 823,-1824 823,-1812 823,-1812 823,-1806 829,-1800 835,-1800 835,-1800 955,-1800 955,-1800 961,-1800 967,-1806 967,-1812 967,-1812 967,-1824 967,-1824 967,-1830 961,-1836 955,-1836"/>
+<text text-anchor="middle" x="895" y="-1815.5" font-family="sans" font-size="10.00">trim_transcriptome_seq_ids</text>
 </g>
 <!-- 18&#45;&gt;13 -->
 <g id="edge24" class="edge">
 <title>18&#45;&gt;13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M900.63,-1799.21C891.03,-1780.18 880.16,-1749.77 894,-1728 901.82,-1715.69 913.34,-1706.2 926.07,-1698.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="927.52,-1702.07 934.81,-1694.38 924.32,-1695.84 927.52,-1702.07"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M895.01,-1799.31C895.86,-1780.07 899.77,-1749.23 915,-1728 923.29,-1716.45 934.95,-1706.92 947.05,-1699.29"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="948.69,-1702.39 955.58,-1694.34 945.18,-1696.33 948.69,-1702.39"/>
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 <!-- 20 -->
 <g id="node21" class="node">
 <title>20</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M1099.5,-1764C1099.5,-1764 914.5,-1764 914.5,-1764 908.5,-1764 902.5,-1758 902.5,-1752 902.5,-1752 902.5,-1740 902.5,-1740 902.5,-1734 908.5,-1728 914.5,-1728 914.5,-1728 1099.5,-1728 1099.5,-1728 1105.5,-1728 1111.5,-1734 1111.5,-1740 1111.5,-1740 1111.5,-1752 1111.5,-1752 1111.5,-1758 1105.5,-1764 1099.5,-1764"/>
-<text text-anchor="middle" x="1007" y="-1743.5" font-family="sans" font-size="10.00">generate_segemehl_index_transcriptome</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1120.5,-1764C1120.5,-1764 935.5,-1764 935.5,-1764 929.5,-1764 923.5,-1758 923.5,-1752 923.5,-1752 923.5,-1740 923.5,-1740 923.5,-1734 929.5,-1728 935.5,-1728 935.5,-1728 1120.5,-1728 1120.5,-1728 1126.5,-1728 1132.5,-1734 1132.5,-1740 1132.5,-1740 1132.5,-1752 1132.5,-1752 1132.5,-1758 1126.5,-1764 1120.5,-1764"/>
+<text text-anchor="middle" x="1028" y="-1743.5" font-family="sans" font-size="10.00">generate_segemehl_index_transcriptome</text>
 </g>
 <!-- 18&#45;&gt;20 -->
 <g id="edge31" class="edge">
 <title>18&#45;&gt;20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M935.47,-1799.15C946.64,-1791.01 960.07,-1781.22 972.27,-1772.33"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="974.11,-1775.32 980.13,-1766.6 969.98,-1769.66 974.11,-1775.32"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M928.91,-1799.15C945.24,-1790.56 965.07,-1780.12 982.68,-1770.85"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="984.26,-1773.98 991.48,-1766.22 981,-1767.78 984.26,-1773.98"/>
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-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M834,-1764C834,-1764 704,-1764 704,-1764 698,-1764 692,-1758 692,-1752 692,-1752 692,-1740 692,-1740 692,-1734 698,-1728 704,-1728 704,-1728 834,-1728 834,-1728 840,-1728 846,-1734 846,-1740 846,-1740 846,-1752 846,-1752 846,-1758 840,-1764 834,-1764"/>
-<text text-anchor="middle" x="769" y="-1743.5" font-family="sans" font-size="10.00">map_transcriptome_oligomap</text>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M855,-1764C855,-1764 725,-1764 725,-1764 719,-1764 713,-1758 713,-1752 713,-1752 713,-1740 713,-1740 713,-1734 719,-1728 725,-1728 725,-1728 855,-1728 855,-1728 861,-1728 867,-1734 867,-1740 867,-1740 867,-1752 867,-1752 867,-1758 861,-1764 855,-1764"/>
+<text text-anchor="middle" x="790" y="-1743.5" font-family="sans" font-size="10.00">map_transcriptome_oligomap</text>
 </g>
-<!-- 18&#45;&gt;22 -->
+<!-- 18&#45;&gt;23 -->
 <g id="edge35" class="edge">
-<title>18&#45;&gt;22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M874.8,-1799.15C857.11,-1790.43 835.59,-1779.82 816.58,-1770.46"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="818.37,-1767.43 807.85,-1766.15 815.27,-1773.71 818.37,-1767.43"/>
+<title>18&#45;&gt;23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M868.23,-1799.15C855.77,-1790.84 840.73,-1780.82 827.18,-1771.79"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="829.5,-1769.13 819.24,-1766.49 825.62,-1774.95 829.5,-1769.13"/>
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 <!-- 19&#45;&gt;18 -->
 <g id="edge29" class="edge">
 <title>19&#45;&gt;18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M917.73,-1871.34C916.88,-1864.75 915.9,-1857.08 914.94,-1849.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="918.43,-1849.38 913.69,-1839.9 911.49,-1850.27 918.43,-1849.38"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M772.81,-1871.15C793.55,-1862.3 818.84,-1851.51 841.03,-1842.04"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="842.38,-1845.27 850.2,-1838.12 839.63,-1838.83 842.38,-1845.27"/>
 </g>
 <!-- 20&#45;&gt;13 -->
-<g id="edge25" class="edge">
+<g id="edge23" class="edge">
 <title>20&#45;&gt;13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1007,-1727.34C1007,-1720.75 1007,-1713.08 1007,-1705.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1010.5,-1705.93 1007,-1695.93 1003.5,-1705.93 1010.5,-1705.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1021.44,-1727.34C1018.93,-1720.59 1016,-1712.69 1013.18,-1705.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1016.47,-1703.9 1009.7,-1695.74 1009.9,-1706.33 1016.47,-1703.9"/>
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 <g id="node22" class="node">
 <title>21</title>
-<path fill="none" stroke="#68d856" stroke-width="2" d="M905.5,-1620C905.5,-1620 762.5,-1620 762.5,-1620 756.5,-1620 750.5,-1614 750.5,-1608 750.5,-1608 750.5,-1596 750.5,-1596 750.5,-1590 756.5,-1584 762.5,-1584 762.5,-1584 905.5,-1584 905.5,-1584 911.5,-1584 917.5,-1590 917.5,-1596 917.5,-1596 917.5,-1608 917.5,-1608 917.5,-1614 911.5,-1620 905.5,-1620"/>
-<text text-anchor="middle" x="834" y="-1599.5" font-family="sans" font-size="10.00">oligomap_transcriptome_to_sam</text>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M947.5,-1620C947.5,-1620 764.5,-1620 764.5,-1620 758.5,-1620 752.5,-1614 752.5,-1608 752.5,-1608 752.5,-1596 752.5,-1596 752.5,-1590 758.5,-1584 764.5,-1584 764.5,-1584 947.5,-1584 947.5,-1584 953.5,-1584 959.5,-1590 959.5,-1596 959.5,-1596 959.5,-1608 959.5,-1608 959.5,-1614 953.5,-1620 947.5,-1620"/>
+<text text-anchor="middle" x="856" y="-1599.5" font-family="sans" font-size="10.00">convert_transcriptome_to_sam_oligomap</text>
 </g>
 <!-- 21&#45;&gt;12 -->
-<g id="edge21" class="edge">
+<g id="edge22" class="edge">
 <title>21&#45;&gt;12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M856.96,-1583.34C867.44,-1575.27 880.06,-1565.57 891.57,-1556.72"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="893.54,-1559.62 899.33,-1550.75 889.27,-1554.07 893.54,-1559.62"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M859.28,-1583.34C860.5,-1576.75 861.93,-1569.08 863.3,-1561.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="866.74,-1562.35 865.12,-1551.88 859.86,-1561.07 866.74,-1562.35"/>
+</g>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M880,-1692C880,-1692 752,-1692 752,-1692 746,-1692 740,-1686 740,-1680 740,-1680 740,-1668 740,-1668 740,-1662 746,-1656 752,-1656 752,-1656 880,-1656 880,-1656 886,-1656 892,-1662 892,-1668 892,-1668 892,-1680 892,-1680 892,-1686 886,-1692 880,-1692"/>
+<text text-anchor="middle" x="816" y="-1671.5" font-family="sans" font-size="10.00">sort_transcriptome_oligomap</text>
 </g>
 <!-- 22&#45;&gt;21 -->
 <g id="edge32" class="edge">
 <title>22&#45;&gt;21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M758.04,-1727.23C748.01,-1708.48 736.47,-1678.57 749,-1656 755.46,-1644.36 765.65,-1634.94 776.77,-1627.46"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="778.31,-1630.62 785.04,-1622.44 774.67,-1624.64 778.31,-1630.62"/>
-</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M898,-1692C898,-1692 770,-1692 770,-1692 764,-1692 758,-1686 758,-1680 758,-1680 758,-1668 758,-1668 758,-1662 764,-1656 770,-1656 770,-1656 898,-1656 898,-1656 904,-1656 910,-1662 910,-1668 910,-1668 910,-1680 910,-1680 910,-1686 904,-1692 898,-1692"/>
-<text text-anchor="middle" x="834" y="-1671.5" font-family="sans" font-size="10.00">sort_transcriptome_oligomap</text>
-</g>
-<!-- 22&#45;&gt;24 -->
-<g id="edge37" class="edge">
-<title>22&#45;&gt;24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M785.4,-1727.34C792.43,-1719.77 800.8,-1710.75 808.6,-1702.35"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="811.08,-1704.83 815.32,-1695.12 805.95,-1700.07 811.08,-1704.83"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M826.09,-1655.34C830.14,-1648.26 834.9,-1639.92 839.43,-1632"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="842.35,-1633.95 844.27,-1623.53 836.27,-1630.48 842.35,-1633.95"/>
 </g>
 <!-- 23&#45;&gt;22 -->
-<g id="edge34" class="edge">
+<g id="edge33" class="edge">
 <title>23&#45;&gt;22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M769,-1799.34C769,-1792.75 769,-1785.08 769,-1777.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="772.5,-1777.93 769,-1767.93 765.5,-1777.93 772.5,-1777.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M796.56,-1727.34C799.07,-1720.59 802,-1712.69 804.82,-1705.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="808.1,-1706.33 808.3,-1695.74 801.53,-1703.9 808.1,-1706.33"/>
 </g>
-<!-- 23&#45;&gt;33 -->
-<g id="edge50" class="edge">
-<title>23&#45;&gt;33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M702.64,-1799.06C667.36,-1789.53 623.8,-1777.76 587.03,-1767.82"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="588.34,-1764.55 577.77,-1765.32 586.51,-1771.3 588.34,-1764.55"/>
+<!-- 24&#45;&gt;23 -->
+<g id="edge34" class="edge">
+<title>24&#45;&gt;23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M751.87,-1799.34C757.2,-1792.01 763.53,-1783.34 769.47,-1775.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="772.11,-1777.49 775.17,-1767.35 766.46,-1773.37 772.11,-1777.49"/>
 </g>
-<!-- 24&#45;&gt;21 -->
-<g id="edge33" class="edge">
-<title>24&#45;&gt;21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M834,-1655.34C834,-1648.75 834,-1641.08 834,-1633.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="837.5,-1633.93 834,-1623.93 830.5,-1633.93 837.5,-1633.93"/>
+<!-- 24&#45;&gt;34 -->
+<g id="edge48" class="edge">
+<title>24&#45;&gt;34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M711.47,-1799.15C698.65,-1790.84 683.18,-1780.82 669.25,-1771.79"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="671.32,-1768.96 661.02,-1766.46 667.51,-1774.83 671.32,-1768.96"/>
 </g>
 <!-- 25 -->
 <g id="node26" class="node">
 <title>25</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M790,-1404C790,-1404 716,-1404 716,-1404 710,-1404 704,-1398 704,-1392 704,-1392 704,-1380 704,-1380 704,-1374 710,-1368 716,-1368 716,-1368 790,-1368 790,-1368 796,-1368 802,-1374 802,-1380 802,-1380 802,-1392 802,-1392 802,-1398 796,-1404 790,-1404"/>
-<text text-anchor="middle" x="753" y="-1383.5" font-family="sans" font-size="10.00">exons_gtf_to_bed</text>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M733.5,-1404C733.5,-1404 618.5,-1404 618.5,-1404 612.5,-1404 606.5,-1398 606.5,-1392 606.5,-1392 606.5,-1380 606.5,-1380 606.5,-1374 612.5,-1368 618.5,-1368 618.5,-1368 733.5,-1368 733.5,-1368 739.5,-1368 745.5,-1374 745.5,-1380 745.5,-1380 745.5,-1392 745.5,-1392 745.5,-1398 739.5,-1404 733.5,-1404"/>
+<text text-anchor="middle" x="676" y="-1383.5" font-family="sans" font-size="10.00">convert_exons_gtf_to_bed</text>
 </g>
 <!-- 25&#45;&gt;9 -->
-<g id="edge18" class="edge">
+<g id="edge17" class="edge">
 <title>25&#45;&gt;9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M762.84,-1367.34C766.74,-1360.34 771.32,-1352.12 775.69,-1344.28"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="778.74,-1345.99 780.55,-1335.55 772.63,-1342.58 778.74,-1345.99"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M695.43,-1367.34C704.03,-1359.52 714.32,-1350.16 723.81,-1341.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="726.02,-1344.25 731.07,-1334.94 721.31,-1339.07 726.02,-1344.25"/>
 </g>
 <!-- 26 -->
 <g id="node27" class="node">
 <title>26</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M782,-1476C782,-1476 724,-1476 724,-1476 718,-1476 712,-1470 712,-1464 712,-1464 712,-1452 712,-1452 712,-1446 718,-1440 724,-1440 724,-1440 782,-1440 782,-1440 788,-1440 794,-1446 794,-1452 794,-1452 794,-1464 794,-1464 794,-1470 788,-1476 782,-1476"/>
-<text text-anchor="middle" x="753" y="-1455.5" font-family="sans" font-size="10.00">get_exons_gtf</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M705,-1476C705,-1476 647,-1476 647,-1476 641,-1476 635,-1470 635,-1464 635,-1464 635,-1452 635,-1452 635,-1446 641,-1440 647,-1440 647,-1440 705,-1440 705,-1440 711,-1440 717,-1446 717,-1452 717,-1452 717,-1464 717,-1464 717,-1470 711,-1476 705,-1476"/>
+<text text-anchor="middle" x="676" y="-1455.5" font-family="sans" font-size="10.00">get_exons_gtf</text>
 </g>
 <!-- 26&#45;&gt;25 -->
-<g id="edge38" class="edge">
+<g id="edge37" class="edge">
 <title>26&#45;&gt;25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M753,-1439.34C753,-1432.75 753,-1425.08 753,-1417.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="756.5,-1417.93 753,-1407.93 749.5,-1417.93 756.5,-1417.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M676,-1439.34C676,-1432.75 676,-1425.08 676,-1417.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="679.5,-1417.93 676,-1407.93 672.5,-1417.93 679.5,-1417.93"/>
 </g>
 <!-- 27 -->
 <g id="node28" class="node">
 <title>27</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M677,-1332C677,-1332 517,-1332 517,-1332 511,-1332 505,-1326 505,-1320 505,-1320 505,-1308 505,-1308 505,-1302 511,-1296 517,-1296 517,-1296 677,-1296 677,-1296 683,-1296 689,-1302 689,-1308 689,-1308 689,-1320 689,-1320 689,-1326 683,-1332 677,-1332"/>
-<text text-anchor="middle" x="597" y="-1311.5" font-family="sans" font-size="10.00">remove_header_genome_mappings</text>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M638,-1332C638,-1332 478,-1332 478,-1332 472,-1332 466,-1326 466,-1320 466,-1320 466,-1308 466,-1308 466,-1302 472,-1296 478,-1296 478,-1296 638,-1296 638,-1296 644,-1296 650,-1302 650,-1308 650,-1308 650,-1320 650,-1320 650,-1326 644,-1332 638,-1332"/>
+<text text-anchor="middle" x="558" y="-1311.5" font-family="sans" font-size="10.00">remove_header_genome_mappings</text>
 </g>
 <!-- 27&#45;&gt;8 -->
 <g id="edge15" class="edge">
 <title>27&#45;&gt;8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M597,-1295.34C597,-1288.75 597,-1281.08 597,-1273.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="600.5,-1273.93 597,-1263.93 593.5,-1273.93 600.5,-1273.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M558,-1295.34C558,-1288.75 558,-1281.08 558,-1273.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="561.5,-1273.93 558,-1263.93 554.5,-1273.93 561.5,-1273.93"/>
 </g>
 <!-- 28 -->
 <g id="node29" class="node">
 <title>28</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M642.5,-1476C642.5,-1476 551.5,-1476 551.5,-1476 545.5,-1476 539.5,-1470 539.5,-1464 539.5,-1464 539.5,-1452 539.5,-1452 539.5,-1446 545.5,-1440 551.5,-1440 551.5,-1440 642.5,-1440 642.5,-1440 648.5,-1440 654.5,-1446 654.5,-1452 654.5,-1452 654.5,-1464 654.5,-1464 654.5,-1470 648.5,-1476 642.5,-1476"/>
-<text text-anchor="middle" x="597" y="-1455.5" font-family="sans" font-size="10.00">filter_genome_by_nh</text>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M603.5,-1476C603.5,-1476 512.5,-1476 512.5,-1476 506.5,-1476 500.5,-1470 500.5,-1464 500.5,-1464 500.5,-1452 500.5,-1452 500.5,-1446 506.5,-1440 512.5,-1440 512.5,-1440 603.5,-1440 603.5,-1440 609.5,-1440 615.5,-1446 615.5,-1452 615.5,-1452 615.5,-1464 615.5,-1464 615.5,-1470 609.5,-1476 603.5,-1476"/>
+<text text-anchor="middle" x="558" y="-1455.5" font-family="sans" font-size="10.00">filter_genome_by_nh</text>
 </g>
 <!-- 28&#45;&gt;27 -->
-<g id="edge39" class="edge">
+<g id="edge38" class="edge">
 <title>28&#45;&gt;27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M597,-1439.02C597,-1415.54 597,-1374.11 597,-1345.64"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="600.5,-1345.87 597,-1335.87 593.5,-1345.87 600.5,-1345.87"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M558,-1439.02C558,-1415.54 558,-1374.11 558,-1345.64"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="561.5,-1345.87 558,-1335.87 554.5,-1345.87 561.5,-1345.87"/>
 </g>
 <!-- 29 -->
 <g id="node30" class="node">
 <title>29</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M645,-1548C645,-1548 549,-1548 549,-1548 543,-1548 537,-1542 537,-1536 537,-1536 537,-1524 537,-1524 537,-1518 543,-1512 549,-1512 549,-1512 645,-1512 645,-1512 651,-1512 657,-1518 657,-1524 657,-1524 657,-1536 657,-1536 657,-1542 651,-1548 645,-1548"/>
-<text text-anchor="middle" x="597" y="-1527.5" font-family="sans" font-size="10.00">merge_genome_maps</text>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M606,-1548C606,-1548 510,-1548 510,-1548 504,-1548 498,-1542 498,-1536 498,-1536 498,-1524 498,-1524 498,-1518 504,-1512 510,-1512 510,-1512 606,-1512 606,-1512 612,-1512 618,-1518 618,-1524 618,-1524 618,-1536 618,-1536 618,-1542 612,-1548 606,-1548"/>
+<text text-anchor="middle" x="558" y="-1527.5" font-family="sans" font-size="10.00">merge_genome_maps</text>
 </g>
 <!-- 29&#45;&gt;28 -->
-<g id="edge40" class="edge">
+<g id="edge39" class="edge">
 <title>29&#45;&gt;28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M597,-1511.34C597,-1504.75 597,-1497.08 597,-1489.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="600.5,-1489.93 597,-1479.93 593.5,-1489.93 600.5,-1489.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M558,-1511.34C558,-1504.75 558,-1497.08 558,-1489.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="561.5,-1489.93 558,-1479.93 554.5,-1489.93 561.5,-1489.93"/>
 </g>
 <!-- 30&#45;&gt;29 -->
 <g id="edge41" class="edge">
 <title>30&#45;&gt;29</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M617.62,-1799.11C613.97,-1751.56 603.97,-1621.6 599.37,-1561.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="602.86,-1561.6 598.61,-1551.9 595.89,-1562.14 602.86,-1561.6"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M511.32,-1799.07C510.29,-1759.46 510.38,-1661.85 532,-1584 534.2,-1576.06 537.59,-1567.88 541.2,-1560.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="544.22,-1562.15 545.71,-1551.66 538.01,-1558.94 544.22,-1562.15"/>
 </g>
 <!-- 31&#45;&gt;30 -->
-<g id="edge45" class="edge">
+<g id="edge42" class="edge">
 <title>31&#45;&gt;30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M572.65,-1871.34C579.28,-1863.85 587.16,-1854.95 594.53,-1846.63"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="597.13,-1848.97 601.14,-1839.17 591.89,-1844.33 597.13,-1848.97"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M512,-1871.34C512,-1864.75 512,-1857.08 512,-1849.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="515.5,-1849.93 512,-1839.93 508.5,-1849.93 515.5,-1849.93"/>
 </g>
 <!-- 32 -->
 <g id="node33" class="node">
 <title>32</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M580,-1620C580,-1620 464,-1620 464,-1620 458,-1620 452,-1614 452,-1608 452,-1608 452,-1596 452,-1596 452,-1590 458,-1584 464,-1584 464,-1584 580,-1584 580,-1584 586,-1584 592,-1590 592,-1596 592,-1596 592,-1608 592,-1608 592,-1614 586,-1620 580,-1620"/>
-<text text-anchor="middle" x="522" y="-1599.5" font-family="sans" font-size="10.00">oligomap_genome_to_sam</text>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M709.5,-1620C709.5,-1620 552.5,-1620 552.5,-1620 546.5,-1620 540.5,-1614 540.5,-1608 540.5,-1608 540.5,-1596 540.5,-1596 540.5,-1590 546.5,-1584 552.5,-1584 552.5,-1584 709.5,-1584 709.5,-1584 715.5,-1584 721.5,-1590 721.5,-1596 721.5,-1596 721.5,-1608 721.5,-1608 721.5,-1614 715.5,-1620 709.5,-1620"/>
+<text text-anchor="middle" x="631" y="-1599.5" font-family="sans" font-size="10.00">convert_genome_to_sam_oligomap</text>
 </g>
 <!-- 32&#45;&gt;29 -->
-<g id="edge42" class="edge">
+<g id="edge40" class="edge">
 <title>32&#45;&gt;29</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M540.93,-1583.34C549.3,-1575.52 559.33,-1566.16 568.57,-1557.53"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="570.68,-1560.35 575.61,-1550.97 565.91,-1555.23 570.68,-1560.35"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M612.58,-1583.34C604.51,-1575.6 594.87,-1566.36 585.96,-1557.81"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="588.49,-1555.39 578.85,-1551 583.65,-1560.44 588.49,-1555.39"/>
+</g>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#d85e56" stroke-width="2" d="M682,-1692C682,-1692 580,-1692 580,-1692 574,-1692 568,-1686 568,-1680 568,-1680 568,-1668 568,-1668 568,-1662 574,-1656 580,-1656 580,-1656 682,-1656 682,-1656 688,-1656 694,-1662 694,-1668 694,-1668 694,-1680 694,-1680 694,-1686 688,-1692 682,-1692"/>
+<text text-anchor="middle" x="631" y="-1671.5" font-family="sans" font-size="10.00">sort_genome_oligomap</text>
 </g>
 <!-- 33&#45;&gt;32 -->
-<g id="edge47" class="edge">
+<g id="edge46" class="edge">
 <title>33&#45;&gt;32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M535.31,-1727.06C546,-1717.92 557.27,-1705.83 563,-1692 569.12,-1677.22 568.17,-1671.14 563,-1656 559.93,-1647.02 554.66,-1638.38 548.89,-1630.78"/>
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-<g id="node35" class="node">
-<title>34</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M542,-1692C542,-1692 440,-1692 440,-1692 434,-1692 428,-1686 428,-1680 428,-1680 428,-1668 428,-1668 428,-1662 434,-1656 440,-1656 440,-1656 542,-1656 542,-1656 548,-1656 554,-1662 554,-1668 554,-1668 554,-1680 554,-1680 554,-1686 548,-1692 542,-1692"/>
-<text text-anchor="middle" x="491" y="-1671.5" font-family="sans" font-size="10.00">sort_genome_oligomap</text>
-</g>
-<!-- 33&#45;&gt;34 -->
-<g id="edge51" class="edge">
-<title>33&#45;&gt;34</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M505.21,-1727.34C503.4,-1720.67 501.28,-1712.89 499.25,-1705.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="502.65,-1704.56 496.65,-1695.82 495.89,-1706.39 502.65,-1704.56"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M631,-1655.34C631,-1648.75 631,-1641.08 631,-1633.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="634.5,-1633.93 631,-1623.93 627.5,-1633.93 634.5,-1633.93"/>
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-<!-- 34&#45;&gt;32 -->
-<g id="edge48" class="edge">
-<title>34&#45;&gt;32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M498.82,-1655.34C501.88,-1648.43 505.48,-1640.31 508.91,-1632.56"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="512,-1634.23 512.85,-1623.67 505.6,-1631.4 512,-1634.23"/>
+<!-- 34&#45;&gt;33 -->
+<g id="edge47" class="edge">
+<title>34&#45;&gt;33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M631,-1727.34C631,-1720.75 631,-1713.08 631,-1705.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="634.5,-1705.93 631,-1695.93 627.5,-1705.93 634.5,-1705.93"/>
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 <!-- 35 -->
 <g id="node36" class="node">
 <title>35</title>
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-<text text-anchor="middle" x="503" y="-735.5" font-family="sans" font-size="10.00">intersect_extended_primir</text>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M600,-756C600,-756 484,-756 484,-756 478,-756 472,-750 472,-744 472,-744 472,-732 472,-732 472,-726 478,-720 484,-720 484,-720 600,-720 600,-720 606,-720 612,-726 612,-732 612,-732 612,-744 612,-744 612,-750 606,-756 600,-756"/>
+<text text-anchor="middle" x="542" y="-735.5" font-family="sans" font-size="10.00">intersect_extended_primir</text>
 </g>
 <!-- 35&#45;&gt;1 -->
-<g id="edge7" class="edge">
+<g id="edge8" class="edge">
 <title>35&#45;&gt;1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M443.81,-719.06C413.11,-709.76 375.38,-698.33 343.11,-688.55"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="344.52,-685.32 333.93,-685.77 342.49,-692.02 344.52,-685.32"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M482.81,-719.06C452.11,-709.76 414.38,-698.33 382.11,-688.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="383.52,-685.32 372.93,-685.77 381.49,-692.02 383.52,-685.32"/>
 </g>
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 <g id="node51" class="node">
 <title>50</title>
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-<text text-anchor="middle" x="503" y="-591.5" font-family="sans" font-size="10.00">quantify_primir</text>
+<path fill="none" stroke="#565bd8" stroke-width="2" d="M574,-612C574,-612 510,-612 510,-612 504,-612 498,-606 498,-600 498,-600 498,-588 498,-588 498,-582 504,-576 510,-576 510,-576 574,-576 574,-576 580,-576 586,-582 586,-588 586,-588 586,-600 586,-600 586,-606 580,-612 574,-612"/>
+<text text-anchor="middle" x="542" y="-591.5" font-family="sans" font-size="10.00">quantify_primir</text>
 </g>
 <!-- 35&#45;&gt;50 -->
-<g id="edge72" class="edge">
+<g id="edge70" class="edge">
 <title>35&#45;&gt;50</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M503,-719.02C503,-695.54 503,-654.11 503,-625.64"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="506.5,-625.87 503,-615.87 499.5,-625.87 506.5,-625.87"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M542,-719.02C542,-695.54 542,-654.11 542,-625.64"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="545.5,-625.87 542,-615.87 538.5,-625.87 545.5,-625.87"/>
 </g>
 <!-- 36 -->
 <g id="node37" class="node">
 <title>36</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M622,-828C622,-828 492,-828 492,-828 486,-828 480,-822 480,-816 480,-816 480,-804 480,-804 480,-798 486,-792 492,-792 492,-792 622,-792 622,-792 628,-792 634,-798 634,-804 634,-804 634,-816 634,-816 634,-822 628,-828 622,-828"/>
-<text text-anchor="middle" x="557" y="-807.5" font-family="sans" font-size="10.00">sort_all_alns_bam_by_position</text>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M652,-828C652,-828 522,-828 522,-828 516,-828 510,-822 510,-816 510,-816 510,-804 510,-804 510,-798 516,-792 522,-792 522,-792 652,-792 652,-792 658,-792 664,-798 664,-804 664,-804 664,-816 664,-816 664,-822 658,-828 652,-828"/>
+<text text-anchor="middle" x="587" y="-807.5" font-family="sans" font-size="10.00">sort_all_alns_bam_by_position</text>
 </g>
 <!-- 36&#45;&gt;35 -->
-<g id="edge53" class="edge">
+<g id="edge51" class="edge">
 <title>36&#45;&gt;35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M543.37,-791.34C537.73,-784.01 531.03,-775.34 524.74,-767.18"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="527.54,-765.08 518.66,-759.3 522,-769.35 527.54,-765.08"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M575.64,-791.34C571.04,-784.18 565.61,-775.73 560.47,-767.73"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="563.5,-765.97 555.15,-759.45 557.61,-769.75 563.5,-765.97"/>
 </g>
 <!-- 37&#45;&gt;36 -->
-<g id="edge54" class="edge">
+<g id="edge52" class="edge">
 <title>37&#45;&gt;36</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M548.78,-863.34C549.81,-856.75 551.02,-849.08 552.18,-841.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="555.62,-842.31 553.72,-831.89 548.71,-841.23 555.62,-842.31"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M578.78,-863.34C579.81,-856.75 581.02,-849.08 582.18,-841.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="585.62,-842.31 583.72,-831.89 578.71,-841.23 585.62,-842.31"/>
 </g>
 <!-- 38 -->
 <g id="node39" class="node">
 <title>38</title>
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M449.5,-828C449.5,-828 340.5,-828 340.5,-828 334.5,-828 328.5,-822 328.5,-816 328.5,-816 328.5,-804 328.5,-804 328.5,-798 334.5,-792 340.5,-792 340.5,-792 449.5,-792 449.5,-792 455.5,-792 461.5,-798 461.5,-804 461.5,-804 461.5,-816 461.5,-816 461.5,-822 455.5,-828 449.5,-828"/>
-<text text-anchor="middle" x="395" y="-807.5" font-family="sans" font-size="10.00">extend_mirs_annotations</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M479.5,-828C479.5,-828 370.5,-828 370.5,-828 364.5,-828 358.5,-822 358.5,-816 358.5,-816 358.5,-804 358.5,-804 358.5,-798 364.5,-792 370.5,-792 370.5,-792 479.5,-792 479.5,-792 485.5,-792 491.5,-798 491.5,-804 491.5,-804 491.5,-816 491.5,-816 491.5,-822 485.5,-828 479.5,-828"/>
+<text text-anchor="middle" x="425" y="-807.5" font-family="sans" font-size="10.00">extend_mirs_annotations</text>
 </g>
 <!-- 38&#45;&gt;35 -->
-<g id="edge52" class="edge">
+<g id="edge50" class="edge">
 <title>38&#45;&gt;35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M422.53,-791.15C435.35,-782.84 450.82,-772.82 464.75,-763.79"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="466.49,-766.83 472.98,-758.46 462.68,-760.96 466.49,-766.83"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M454.83,-791.15C468.99,-782.68 486.14,-772.42 501.46,-763.25"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="502.85,-766.5 509.63,-758.37 499.25,-760.5 502.85,-766.5"/>
 </g>
 <!-- 43 -->
 <g id="node44" class="node">
 <title>43</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M377,-468C377,-468 263,-468 263,-468 257,-468 251,-462 251,-456 251,-456 251,-444 251,-444 251,-438 257,-432 263,-432 263,-432 377,-432 377,-432 383,-432 389,-438 389,-444 389,-444 389,-456 389,-456 389,-462 383,-468 377,-468"/>
-<text text-anchor="middle" x="320" y="-447.5" font-family="sans" font-size="10.00">intersect_extended_mirna</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M413,-468C413,-468 299,-468 299,-468 293,-468 287,-462 287,-456 287,-456 287,-444 287,-444 287,-438 293,-432 299,-432 299,-432 413,-432 413,-432 419,-432 425,-438 425,-444 425,-444 425,-456 425,-456 425,-462 419,-468 413,-468"/>
+<text text-anchor="middle" x="356" y="-447.5" font-family="sans" font-size="10.00">intersect_extended_mirna</text>
 </g>
 <!-- 38&#45;&gt;43 -->
-<g id="edge63" class="edge">
+<g id="edge60" class="edge">
 <title>38&#45;&gt;43</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M397.07,-791.1C400,-764.2 405,-711.73 405,-667 405,-667 405,-667 405,-593 405,-552.55 407.22,-538.43 386,-504 379.6,-493.62 370.42,-484.4 360.92,-476.68"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="363.13,-473.95 353.04,-470.73 358.91,-479.54 363.13,-473.95"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M428.94,-791.17C434.5,-764.36 444,-712.02 444,-667 444,-667 444,-667 444,-593 444,-552.55 446.59,-538.2 425,-504 418.3,-493.38 408.67,-484.07 398.73,-476.34"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="400.98,-473.64 390.82,-470.63 396.88,-479.32 400.98,-473.64"/>
 </g>
 <!-- 39 -->
 <g id="node40" class="node">
 <title>39</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M439,-900C439,-900 371,-900 371,-900 365,-900 359,-894 359,-888 359,-888 359,-876 359,-876 359,-870 365,-864 371,-864 371,-864 439,-864 439,-864 445,-864 451,-870 451,-876 451,-876 451,-888 451,-888 451,-894 445,-900 439,-900"/>
-<text text-anchor="middle" x="405" y="-879.5" font-family="sans" font-size="10.00">map_chr_names</text>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M459,-900C459,-900 391,-900 391,-900 385,-900 379,-894 379,-888 379,-888 379,-876 379,-876 379,-870 385,-864 391,-864 391,-864 459,-864 459,-864 465,-864 471,-870 471,-876 471,-876 471,-888 471,-888 471,-894 465,-900 459,-900"/>
+<text text-anchor="middle" x="425" y="-879.5" font-family="sans" font-size="10.00">map_chr_names</text>
 </g>
 <!-- 39&#45;&gt;38 -->
-<g id="edge57" class="edge">
+<g id="edge54" class="edge">
 <title>39&#45;&gt;38</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M402.48,-863.34C401.54,-856.75 400.44,-849.08 399.38,-841.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="402.86,-841.3 397.99,-831.9 395.93,-842.29 402.86,-841.3"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M425,-863.34C425,-856.75 425,-849.08 425,-841.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="428.5,-841.93 425,-831.93 421.5,-841.93 428.5,-841.93"/>
 </g>
 <!-- 40 -->
 <g id="node41" class="node">
 <title>40</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M362,-1188C362,-1188 300,-1188 300,-1188 294,-1188 288,-1182 288,-1176 288,-1176 288,-1164 288,-1164 288,-1158 294,-1152 300,-1152 300,-1152 362,-1152 362,-1152 368,-1152 374,-1158 374,-1164 374,-1164 374,-1176 374,-1176 374,-1182 368,-1188 362,-1188"/>
-<text text-anchor="middle" x="331" y="-1167.5" font-family="sans" font-size="10.00">extract_chr_len</text>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M323,-1188C323,-1188 261,-1188 261,-1188 255,-1188 249,-1182 249,-1176 249,-1176 249,-1164 249,-1164 249,-1158 255,-1152 261,-1152 261,-1152 323,-1152 323,-1152 329,-1152 335,-1158 335,-1164 335,-1164 335,-1176 335,-1176 335,-1182 329,-1188 323,-1188"/>
+<text text-anchor="middle" x="292" y="-1167.5" font-family="sans" font-size="10.00">extract_chr_len</text>
 </g>
 <!-- 40&#45;&gt;38 -->
-<g id="edge56" class="edge">
+<g id="edge55" class="edge">
 <title>40&#45;&gt;38</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M331,-1151.07C331,-1124.13 331,-1071.62 331,-1027 331,-1027 331,-1027 331,-953 331,-912.55 332.15,-900.29 350,-864 354.45,-854.96 360.77,-846.19 367.28,-838.46"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="369.7,-841.01 373.78,-831.23 364.5,-836.33 369.7,-841.01"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M292,-1151.07C292,-1124.13 292,-1071.62 292,-1027 292,-1027 292,-1027 292,-953 292,-900.74 340.58,-859.78 379.03,-835.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="380.73,-838.61 387.47,-830.44 377.1,-832.62 380.73,-838.61"/>
 </g>
 <!-- 41&#45;&gt;40 -->
-<g id="edge58" class="edge">
+<g id="edge56" class="edge">
 <title>41&#45;&gt;40</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M331,-1223.34C331,-1216.75 331,-1209.08 331,-1201.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="334.5,-1201.93 331,-1191.93 327.5,-1201.93 334.5,-1201.93"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M292,-1223.34C292,-1216.75 292,-1209.08 292,-1201.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="295.5,-1201.93 292,-1191.93 288.5,-1201.93 295.5,-1201.93"/>
 </g>
 <!-- 42&#45;&gt;0 -->
-<g id="edge4" class="edge">
+<g id="edge3" class="edge">
 <title>42&#45;&gt;0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M254.4,-359.25C252.49,-301.99 246.44,-121.72 244.02,-49.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="247.53,-49.76 243.7,-39.89 240.54,-50 247.53,-49.76"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M295.24,-359.08C297,-332.15 300,-279.66 300,-235 300,-235 300,-235 300,-161 300,-119.79 301.95,-102.28 274,-72 248.33,-44.18 206.49,-30.85 175.41,-24.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="176.27,-21.13 165.81,-22.77 175.02,-28.01 176.27,-21.13"/>
 </g>
-<!-- 47 -->
-<g id="node48" class="node">
-<title>47</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M428.5,-324C428.5,-324 307.5,-324 307.5,-324 301.5,-324 295.5,-318 295.5,-312 295.5,-312 295.5,-300 295.5,-300 295.5,-294 301.5,-288 307.5,-288 307.5,-288 428.5,-288 428.5,-288 434.5,-288 440.5,-294 440.5,-300 440.5,-300 440.5,-312 440.5,-312 440.5,-318 434.5,-324 428.5,-324"/>
-<text text-anchor="middle" x="368" y="-303.5" font-family="sans" font-size="10.00">add_intersecting_mirna_tag</text>
+<!-- 49 -->
+<g id="node50" class="node">
+<title>49</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M467.5,-324C467.5,-324 346.5,-324 346.5,-324 340.5,-324 334.5,-318 334.5,-312 334.5,-312 334.5,-300 334.5,-300 334.5,-294 340.5,-288 346.5,-288 346.5,-288 467.5,-288 467.5,-288 473.5,-288 479.5,-294 479.5,-300 479.5,-300 479.5,-312 479.5,-312 479.5,-318 473.5,-324 467.5,-324"/>
+<text text-anchor="middle" x="407" y="-303.5" font-family="sans" font-size="10.00">add_intersecting_mirna_tag</text>
 </g>
-<!-- 42&#45;&gt;47 -->
-<g id="edge67" class="edge">
-<title>42&#45;&gt;47</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M283.81,-359.15C297.35,-350.76 313.72,-340.62 328.41,-331.52"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="330.01,-334.65 336.67,-326.41 326.33,-328.7 330.01,-334.65"/>
+<!-- 42&#45;&gt;49 -->
+<g id="edge68" class="edge">
+<title>42&#45;&gt;49</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M322.81,-359.15C336.35,-350.76 352.72,-340.62 367.41,-331.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="369.01,-334.65 375.67,-326.41 365.33,-328.7 369.01,-334.65"/>
 </g>
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-<g id="node54" class="node">
-<title>53</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M193.5,-324C193.5,-324 122.5,-324 122.5,-324 116.5,-324 110.5,-318 110.5,-312 110.5,-312 110.5,-300 110.5,-300 110.5,-294 116.5,-288 122.5,-288 122.5,-288 193.5,-288 193.5,-288 199.5,-288 205.5,-294 205.5,-300 205.5,-300 205.5,-312 205.5,-312 205.5,-318 199.5,-324 193.5,-324"/>
-<text text-anchor="middle" x="158" y="-303.5" font-family="sans" font-size="10.00">uncollapse_reads</text>
+<!-- 51 -->
+<g id="node52" class="node">
+<title>51</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M204.5,-324C204.5,-324 133.5,-324 133.5,-324 127.5,-324 121.5,-318 121.5,-312 121.5,-312 121.5,-300 121.5,-300 121.5,-294 127.5,-288 133.5,-288 133.5,-288 204.5,-288 204.5,-288 210.5,-288 216.5,-294 216.5,-300 216.5,-300 216.5,-312 216.5,-312 216.5,-318 210.5,-324 204.5,-324"/>
+<text text-anchor="middle" x="169" y="-303.5" font-family="sans" font-size="10.00">uncollapse_reads</text>
 </g>
-<!-- 42&#45;&gt;53 -->
-<g id="edge75" class="edge">
-<title>42&#45;&gt;53</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M230.27,-359.15C218.98,-351.01 205.41,-341.22 193.1,-332.33"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="195.29,-329.6 185.14,-326.58 191.2,-335.27 195.29,-329.6"/>
+<!-- 42&#45;&gt;51 -->
+<g id="edge71" class="edge">
+<title>42&#45;&gt;51</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M262.13,-359.15C246.85,-350.6 228.33,-340.22 211.84,-330.99"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="213.88,-328.12 203.45,-326.29 210.46,-334.23 213.88,-328.12"/>
 </g>
 <!-- 43&#45;&gt;42 -->
-<g id="edge61" class="edge">
+<g id="edge58" class="edge">
 <title>43&#45;&gt;42</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M303.6,-431.34C296.57,-423.77 288.2,-414.75 280.4,-406.35"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="283.05,-404.07 273.68,-399.12 277.92,-408.83 283.05,-404.07"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M340.35,-431.34C333.72,-423.85 325.84,-414.95 318.47,-406.63"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="321.11,-404.33 311.86,-399.17 315.87,-408.97 321.11,-404.33"/>
 </g>
-<!-- 43&#45;&gt;47 -->
-<g id="edge68" class="edge">
-<title>43&#45;&gt;47</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M331.28,-431.46C337.3,-421.42 344.4,-408.39 349,-396 355.99,-377.18 360.72,-355.12 363.71,-337.68"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="367.17,-338.23 365.28,-327.81 360.25,-337.14 367.17,-338.23"/>
+<!-- 43&#45;&gt;49 -->
+<g id="edge69" class="edge">
+<title>43&#45;&gt;49</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M368.84,-431.14C375.44,-421.22 383.1,-408.39 388,-396 395.42,-377.24 400.17,-355.06 403.06,-337.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="406.48,-338.3 404.51,-327.89 399.56,-337.26 406.48,-338.3"/>
 </g>
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 <g id="node45" class="node">
 <title>44</title>
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-<text text-anchor="middle" x="272" y="-519.5" font-family="sans" font-size="10.00">sort_intersecting_primir_bam_by_position</text>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M404,-540C404,-540 218,-540 218,-540 212,-540 206,-534 206,-528 206,-528 206,-516 206,-516 206,-510 212,-504 218,-504 218,-504 404,-504 404,-504 410,-504 416,-510 416,-516 416,-516 416,-528 416,-528 416,-534 410,-540 404,-540"/>
+<text text-anchor="middle" x="311" y="-519.5" font-family="sans" font-size="10.00">sort_intersecting_primir_bam_by_position</text>
 </g>
 <!-- 44&#45;&gt;43 -->
-<g id="edge62" class="edge">
+<g id="edge61" class="edge">
 <title>44&#45;&gt;43</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M284.11,-503.34C289.08,-496.1 294.95,-487.53 300.49,-479.45"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="303.24,-481.62 306.01,-471.4 297.47,-477.67 303.24,-481.62"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M322.36,-503.34C326.96,-496.18 332.39,-487.73 337.53,-479.73"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="340.39,-481.75 342.85,-471.45 334.5,-477.97 340.39,-481.75"/>
 </g>
 <!-- 45&#45;&gt;44 -->
-<g id="edge64" class="edge">
+<g id="edge62" class="edge">
 <title>45&#45;&gt;44</title>
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diff --git a/test/expected_output.md5 b/test/expected_output.md5
index 0f32828..c3fc05e 100644
--- a/test/expected_output.md5
+++ b/test/expected_output.md5
@@ -1,58 +1,58 @@
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+a844e3a29159e36e2f17a0646d1e8c5f  results/intermediates/TABLES/pri-mir_counts_test_lib
+36f7d024fe6ddfd3e788aebf61c61061  results/intermediates/test_lib/oligomap_genome_sorted.fasta
+48e605df55bf2dd37ea5a5a74eb5872a  results/intermediates/test_lib/mappings_all.sam
+d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_mappings.fasta
+e9aac4afeb2053385d60f5e4b07a9774  results/intermediates/test_lib/mappings_all_removed_inferiors.sam
+9ebcb4ac877f37921b88ceca3ff03b62  results/intermediates/test_lib/alignments_intersecting_primir.bam
+defdc8c46e1d73692edde0e0278f2d5e  results/intermediates/test_lib/oligomap_genome_mappings.fasta
+e632f8984d423d46bbb377ec75468521  results/intermediates/test_lib/segemehl_transcriptome_mappings.sam
+e632f8984d423d46bbb377ec75468521  results/intermediates/test_lib/transcriptome_mappings_filtered_nh.sam
+3344bbeb9fe01f07c04831e5b4a795ba  results/intermediates/test_lib/alignments_all.bam
+a124a5afdb5f7bfbcc5683260556c9c4  results/intermediates/test_lib/mappings_all_no_header.sam
+d62630102c33d43d593af14c2a642839  results/intermediates/test_lib/alignments_all.sam
+81103749d61bc55ee2cfc84ca1527456  results/intermediates/test_lib/alignments_intersecting_mirna_tag.sam
+d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_sorted.fasta
+76643f87bb2e2bff77d1b1223d7720b5  results/intermediates/test_lib/segemehl_genome_mappings.sam
+d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/transcriptome_mappings_to_genome.sam
+63a32839360a985b68e0685aafad5c54  results/intermediates/test_lib/fa/reads.fa
+e9e9698d9350b64b64c1f6d96019fce8  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.sam
+edcb854702519c0002d8ce89a21e54ef  results/intermediates/test_lib/reads_formatted.fasta
+1a547487b8e92ad85bb26ff9b1db1f93  results/intermediates/test_lib/intersected_extended_mirna.bed
+a287ffc43b6afbdde3e9905bc27c28a5  results/intermediates/test_lib/alignments_all_sorted_test_lib.bam
+ec0e9bcc8ea857da897035c8fca4078f  results/intermediates/test_lib/reads_trimmed_adapters.fasta
+d7a5ab720ff9c96f41f3755a05b8f9e0  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.bam
+1f1b873d05ec14ef9b16376a1c98315b  results/intermediates/test_lib/genome_mappings.sam
+f5cb65466d328036a15b66cfbd4d8419  results/intermediates/test_lib/oligomap_genome_report.txt
+6cbdb9299e09b3e39b79a50db69226b5  results/intermediates/test_lib/transcriptome_mappings_no_header.sam
+e632f8984d423d46bbb377ec75468521  results/intermediates/test_lib/transcriptome_mappings.sam
+947607be69c16246f8dc9adbd9b971c8  results/intermediates/test_lib/oligomap_genome_mappings.sam
+ce3fcd037e0a6a0b1a7a3253219e7053  results/intermediates/test_lib/alignments_intersecting_mirna_sorted_tag.sam
+53764354c520d9700f13761c2721d8aa  results/intermediates/test_lib/alignments_intersecting_primir_sorted.bam
+d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_mappings.sam
+a124a5afdb5f7bfbcc5683260556c9c4  results/intermediates/test_lib/genome_mappings_no_header.sam
+1f1b873d05ec14ef9b16376a1c98315b  results/intermediates/test_lib/genome_mappings_filtered_nh.sam
+6cc6165e8942a08420552aa810e629f8  results/intermediates/test_lib/mappings_all_sorted_by_id.sam
+2c77ffa021dda190d82f3f54a3312393  results/intermediates/test_lib/reads_collapsed.fasta
+f68693cfaa1e6ea78e1a5562ade6d9ed  results/intermediates/test_lib/intersected_extended_primir.bed
+c2a5770a755ada66ef63d96eec4afb00  results/intermediates/test_lib/reads_filtered_for_oligomap.fasta
+fe5388094985e9604a302d39d2abc82c  results/intermediates/test_lib/oligomap_transcriptome_report.txt
+be7a0d92e57480190de57eb30baffa36  results/intermediates/extended_mirna_annotation_6_nt.gff3
+8148cd880602255be166beb59bbed95a  results/intermediates/genome_header.sam
+09e24a504bfec37fee3d5ff1b5c7738e  results/intermediates/exons.bed
+4fb453846e88593d0cac13220ec2d685  results/intermediates/segemehl_genome_index.idx
+d34fc868b861b1bc46db07a397dc0f10  results/intermediates/genome_processed.fa.fai
+21e102e4ebd3508bb06f46366a3d578d  results/intermediates/exons.gtf
+003b92b245ac336e3d70a513033e1cee  results/intermediates/transcriptome_trimmed_id.fa
+44dbf7c3eae00d0bc8d5e1319123746c  results/intermediates/chr_size.txt
+cc5c3512dab0e269d82bd625de74198e  results/intermediates/extended_primir_annotation_6_nt.gff3
+f28cc0143ab6659bef3de3a7afa1dccc  results/intermediates/mirna_annotations.gff3
+2d437f8681f4248d4f2075f86debb920  results/intermediates/transcriptome.fa
+7eb64c112830266bcf416ded60b4cf77  results/intermediates/segemehl_transcriptome_index.idx
+4fba145540a2c61f29bfddfd0f5a4d4e  results/intermediates/genome_processed.fa
diff --git a/test/test_workflow_local_with_conda.sh b/test/test_workflow_local_with_conda.sh
index 6b17996..20c0555 100755
--- a/test/test_workflow_local_with_conda.sh
+++ b/test/test_workflow_local_with_conda.sh
@@ -25,9 +25,9 @@ snakemake \
     --use-conda \
     --printshellcmds \
     --rerun-incomplete \
+    --no-hooks \
     --verbose
 
-
 # Snakemake report
 snakemake \
     --snakefile="../workflow/Snakefile" \
diff --git a/test/test_workflow_local_with_singularity.sh b/test/test_workflow_local_with_singularity.sh
index 306caac..b8f3dea 100755
--- a/test/test_workflow_local_with_singularity.sh
+++ b/test/test_workflow_local_with_singularity.sh
@@ -26,9 +26,9 @@ snakemake \
     --singularity-args "--bind ${PWD}/../" \
     --printshellcmds \
     --rerun-incomplete \
+    --no-hooks \
     --verbose
 
-
 # Snakemake report
 snakemake \
     --snakefile="../workflow/Snakefile" \
diff --git a/test/test_workflow_slurm_with_conda.sh b/test/test_workflow_slurm_with_conda.sh
index 190ffdc..2e6c715 100755
--- a/test/test_workflow_slurm_with_conda.sh
+++ b/test/test_workflow_slurm_with_conda.sh
@@ -41,6 +41,7 @@ snakemake \
     --use-conda \
     --printshellcmds \
     --rerun-incomplete \
+    --no-hooks \
     --verbose
 
 # Snakemake report
diff --git a/test/test_workflow_slurm_with_singularity.sh b/test/test_workflow_slurm_with_singularity.sh
index 4ea8a9b..88781fd 100755
--- a/test/test_workflow_slurm_with_singularity.sh
+++ b/test/test_workflow_slurm_with_singularity.sh
@@ -42,6 +42,7 @@ snakemake \
     --singularity-args="--bind ${PWD}/../" \
     --printshellcmds \
     --rerun-incomplete \
+    --no-hooks \
     --verbose
 
 # Snakemake report
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 4dcd95c..e9648d6 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -31,6 +31,23 @@ validate(config, Path("../config/config_schema.json"))
 
 
 OUT_DIR = Path(config["output_dir"])
+INTERMEDIATES_DIR = Path(config["intermediates_dir"])
+LOG_DIR = Path(f"{config['local_log']}/../")
+
+
+###############################################################################
+### onSuccess/onError handlers configuration
+###############################################################################
+
+
+onsuccess:
+    print("\nWORKFLOW SUCCEED. Removing intermediate files.\n")
+    shell("rm -rf {INTERMEDIATES_DIR}")
+
+
+onerror:
+    print("\nWORKFLOW FAILED. Check the log file in the log directory.\n")
+    shell("cat {log} > {LOG_DIR}/failed_workflow.log")
 
 
 ###############################################################################
@@ -67,10 +84,6 @@ rule finish:
             OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
             sample=pd.unique(samples_table.index.values),
         ),
-        intersect_sam=expand(
-            OUT_DIR / "{sample}" / "alignments_intersecting_mirna_sorted_tag.sam",
-            sample=pd.unique(samples_table.index.values),
-        ),
         table=expand(
             OUT_DIR / "TABLES" / "all_{mir}_counts.tab",
             mir=[mir for mir in config["mir_list"] if mir != "isomir"],
diff --git a/workflow/rules/map.smk b/workflow/rules/map.smk
index effa9a6..0c1131f 100644
--- a/workflow/rules/map.smk
+++ b/workflow/rules/map.smk
@@ -24,7 +24,7 @@ validate(config, Path("../../config/config_schema.json"))
 
 
 ENV_DIR = Path(f"{workflow.basedir}/envs")
-OUT_DIR = Path(config["output_dir"])
+INTERMEDIATES_DIR = Path(config["intermediates_dir"])
 SCRIPTS_DIR = Path(config["scripts_dir"])
 
 CLUSTER_LOG = Path(config["cluster_log"])
@@ -70,7 +70,7 @@ localrules:
 rule finish_map:
     input:
         maps=expand(
-            OUT_DIR / "{sample}" / "alignments_all_sorted_{sample}.bam.bai",
+            INTERMEDIATES_DIR / "{sample}" / "alignments_all_sorted_{sample}.bam.bai",
             sample=pd.unique(samples_table.index.values),
         ),
 
@@ -87,7 +87,7 @@ rule start:
             format=convert_lib_format(get_sample("format")),
         ),
     output:
-        reads=OUT_DIR / "{sample}" / "{format}" / "reads.{format}",
+        reads=INTERMEDIATES_DIR / "{sample}" / "{format}" / "reads.{format}",
     params:
         cluster_log=CLUSTER_LOG / "uncompress_zipped_files_{sample}_{format}.log",
     log:
@@ -105,9 +105,9 @@ rule start:
 
 rule fastq_quality_filter:
     input:
-        reads=OUT_DIR / "{sample}" / "fastq" / "reads.fastq",
+        reads=INTERMEDIATES_DIR / "{sample}" / "fastq" / "reads.fastq",
     output:
-        reads=OUT_DIR / "{sample}" / "fastq" / "filtered_reads.fastq",
+        reads=INTERMEDIATES_DIR / "{sample}" / "fastq" / "filtered_reads.fastq",
     params:
         cluster_log=CLUSTER_LOG / "fastq_quality_filter_{sample}.log",
         p=config["p_value"],
@@ -135,9 +135,9 @@ rule fastq_quality_filter:
 
 rule fastq_to_fasta:
     input:
-        reads=OUT_DIR / "{sample}" / "fastq" / "filtered_reads.fastq",
+        reads=INTERMEDIATES_DIR / "{sample}" / "fastq" / "filtered_reads.fastq",
     output:
-        reads=OUT_DIR / "{sample}" / "fastq" / "reads.fa",
+        reads=INTERMEDIATES_DIR / "{sample}" / "fastq" / "reads.fa",
     params:
         cluster_log=CLUSTER_LOG / "fastq_to_fasta_{sample}.log",
     log:
@@ -157,12 +157,12 @@ rule fastq_to_fasta:
 
 rule format_fasta:
     input:
-        reads=lambda wildcards: OUT_DIR
+        reads=lambda wildcards: INTERMEDIATES_DIR
         / wildcards.sample
         / convert_lib_format(get_sample("format", wildcards.sample))
         / "reads.fa",
     output:
-        reads=OUT_DIR / "{sample}" / "reads_formatted.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_formatted.fasta",
     params:
         cluster_log=CLUSTER_LOG / "format_fasta_{sample}.log",
     log:
@@ -182,9 +182,9 @@ rule format_fasta:
 
 rule remove_adapters:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_formatted.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_formatted.fasta",
     output:
-        reads=OUT_DIR / "{sample}" / "reads_trimmed_adapters.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_trimmed_adapters.fasta",
     params:
         adapter=lambda wildcards: get_sample("adapter", wildcards.sample).upper(),
         error_rate=config["error_rate"],
@@ -219,9 +219,9 @@ rule remove_adapters:
 
 rule collapse_identical_reads:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_trimmed_adapters.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_trimmed_adapters.fasta",
     output:
-        reads=OUT_DIR / "{sample}" / "reads_collapsed.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_collapsed.fasta",
     params:
         cluster_log=CLUSTER_LOG / "collapse_identical_reads_{sample}.log",
     log:
@@ -241,11 +241,11 @@ rule collapse_identical_reads:
 
 rule map_genome_segemehl:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_collapsed.fasta",
-        genome=OUT_DIR / "genome_processed.fa",
-        genome_index_segemehl=OUT_DIR / "segemehl_genome_index.idx",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_collapsed.fasta",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa",
+        genome_index_segemehl=INTERMEDIATES_DIR / "segemehl_genome_index.idx",
     output:
-        gmap=OUT_DIR / "{sample}" / "segemehl_genome_mappings.sam",
+        gmap=INTERMEDIATES_DIR / "{sample}" / "segemehl_genome_mappings.sam",
     params:
         cluster_log=CLUSTER_LOG / "map_genome_segemehl_{sample}.log",
     log:
@@ -276,11 +276,12 @@ rule map_genome_segemehl:
 
 rule map_transcriptome_segemehl:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_collapsed.fasta",
-        transcriptome=OUT_DIR / "transcriptome_trimmed_id.fa",
-        transcriptome_index_segemehl=OUT_DIR / "segemehl_transcriptome_index.idx",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_collapsed.fasta",
+        transcriptome=INTERMEDIATES_DIR / "transcriptome_trimmed_id.fa",
+        transcriptome_index_segemehl=INTERMEDIATES_DIR
+        / "segemehl_transcriptome_index.idx",
     output:
-        tmap=OUT_DIR / "{sample}" / "segemehl_transcriptome_mappings.sam",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "segemehl_transcriptome_mappings.sam",
     params:
         cluster_log=CLUSTER_LOG / "map_transcriptome_segemehl_{sample}.log",
     log:
@@ -311,10 +312,10 @@ rule map_transcriptome_segemehl:
 
 rule filter_fasta_for_oligomap:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_collapsed.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_collapsed.fasta",
         script=SCRIPTS_DIR / "validation_fasta.py",
     output:
-        reads=OUT_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
     params:
         cluster_log=CLUSTER_LOG / "filter_fasta_for_oligomap_{sample}.log",
         max_length_reads=config["max_length_reads"],
@@ -339,11 +340,11 @@ rule filter_fasta_for_oligomap:
 
 rule map_genome_oligomap:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
-        target=OUT_DIR / "genome_processed.fa",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
+        target=INTERMEDIATES_DIR / "genome_processed.fa",
     output:
-        gmap=OUT_DIR / "{sample}" / "oligomap_genome_mappings.fasta",
-        report=OUT_DIR / "{sample}" / "oligomap_genome_report.txt",
+        gmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.fasta",
+        report=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_report.txt",
     params:
         cluster_log=CLUSTER_LOG / "map_genome_oligomap_{sample}.log",
     log:
@@ -372,11 +373,11 @@ rule map_genome_oligomap:
 
 rule sort_genome_oligomap:
     input:
-        tmap=OUT_DIR / "{sample}" / "oligomap_genome_mappings.fasta",
-        report=OUT_DIR / "{sample}" / "oligomap_genome_report.txt",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.fasta",
+        report=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_report.txt",
         script=SCRIPTS_DIR / "blocksort.sh",
     output:
-        sort=OUT_DIR / "{sample}" / "oligomap_genome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_sorted.fasta",
     params:
         cluster_log=CLUSTER_LOG / "sort_genome_oligomap_{sample}.log",
     log:
@@ -401,10 +402,10 @@ rule sort_genome_oligomap:
 
 rule convert_genome_to_sam_oligomap:
     input:
-        sort=OUT_DIR / "{sample}" / "oligomap_genome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_sorted.fasta",
         script=SCRIPTS_DIR / "oligomap_output_to_sam_nh_filtered.py",
     output:
-        gmap=OUT_DIR / "{sample}" / "oligomap_genome_mappings.sam",
+        gmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.sam",
     params:
         cluster_log=CLUSTER_LOG / "oligomap_genome_to_sam_{sample}.log",
         nh=config["nh"],
@@ -431,11 +432,11 @@ rule convert_genome_to_sam_oligomap:
 
 rule map_transcriptome_oligomap:
     input:
-        reads=OUT_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
-        target=OUT_DIR / "transcriptome_trimmed_id.fa",
+        reads=INTERMEDIATES_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
+        target=INTERMEDIATES_DIR / "transcriptome_trimmed_id.fa",
     output:
-        tmap=OUT_DIR / "{sample}" / "oligomap_transcriptome_mappings.fasta",
-        report=OUT_DIR / "{sample}" / "oligomap_transcriptome_report.txt",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.fasta",
+        report=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_report.txt",
     params:
         cluster_log=CLUSTER_LOG / "map_transcriptome_oligomap_{sample}.log",
     log:
@@ -465,11 +466,11 @@ rule map_transcriptome_oligomap:
 
 rule sort_transcriptome_oligomap:
     input:
-        tmap=OUT_DIR / "{sample}" / "oligomap_transcriptome_mappings.fasta",
-        report=OUT_DIR / "{sample}" / "oligomap_transcriptome_report.txt",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.fasta",
+        report=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_report.txt",
         script=SCRIPTS_DIR / "blocksort.sh",
     output:
-        sort=OUT_DIR / "{sample}" / "oligomap_transcriptome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_sorted.fasta",
     params:
         cluster_log=CLUSTER_LOG / "sort_transcriptome_oligomap_{sample}.log",
     log:
@@ -493,10 +494,10 @@ rule sort_transcriptome_oligomap:
 
 rule convert_transcriptome_to_sam_oligomap:
     input:
-        sort=OUT_DIR / "{sample}" / "oligomap_transcriptome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_sorted.fasta",
         script=SCRIPTS_DIR / "oligomap_output_to_sam_nh_filtered.py",
     output:
-        tmap=OUT_DIR / "{sample}" / "oligomap_transcriptome_mappings.sam",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.sam",
     params:
         cluster_log=CLUSTER_LOG / "oligomap_transcriptome_to_sam_{sample}.log",
         nh=config["nh"],
@@ -520,10 +521,10 @@ rule convert_transcriptome_to_sam_oligomap:
 
 rule merge_genome_maps:
     input:
-        gmap1=OUT_DIR / "{sample}" / "segemehl_genome_mappings.sam",
-        gmap2=OUT_DIR / "{sample}" / "oligomap_genome_mappings.sam",
+        gmap1=INTERMEDIATES_DIR / "{sample}" / "segemehl_genome_mappings.sam",
+        gmap2=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.sam",
     output:
-        gmaps=OUT_DIR / "{sample}" / "genome_mappings.sam",
+        gmaps=INTERMEDIATES_DIR / "{sample}" / "genome_mappings.sam",
     params:
         cluster_log=CLUSTER_LOG / "merge_genome_maps_{sample}.log",
     log:
@@ -541,10 +542,10 @@ rule merge_genome_maps:
 
 rule merge_transcriptome_maps:
     input:
-        tmap1=OUT_DIR / "{sample}" / "segemehl_transcriptome_mappings.sam",
-        tmap2=OUT_DIR / "{sample}" / "oligomap_transcriptome_mappings.sam",
+        tmap1=INTERMEDIATES_DIR / "{sample}" / "segemehl_transcriptome_mappings.sam",
+        tmap2=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.sam",
     output:
-        tmaps=OUT_DIR / "{sample}" / "transcriptome_mappings.sam",
+        tmaps=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings.sam",
     params:
         cluster_log=CLUSTER_LOG / "merge_transcriptome_maps_{sample}.log",
     log:
@@ -562,10 +563,10 @@ rule merge_transcriptome_maps:
 
 rule filter_genome_by_nh:
     input:
-        gmaps=OUT_DIR / "{sample}" / "genome_mappings.sam",
+        gmaps=INTERMEDIATES_DIR / "{sample}" / "genome_mappings.sam",
         script=SCRIPTS_DIR / "nh_filter.py",
     output:
-        gmaps=OUT_DIR / "{sample}" / "genome_mappings_filtered_nh.sam",
+        gmaps=INTERMEDIATES_DIR / "{sample}" / "genome_mappings_filtered_nh.sam",
     params:
         cluster_log=CLUSTER_LOG / "filter_genome_by_nh_{sample}.log",
         nh=config["nh"],
@@ -590,10 +591,10 @@ rule filter_genome_by_nh:
 
 rule filter_transcriptome_by_nh:
     input:
-        tmaps=OUT_DIR / "{sample}" / "transcriptome_mappings.sam",
+        tmaps=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings.sam",
         script=SCRIPTS_DIR / "nh_filter.py",
     output:
-        tmaps=OUT_DIR / "{sample}" / "transcriptome_mappings_filtered_nh.sam",
+        tmaps=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings_filtered_nh.sam",
     params:
         cluster_log=CLUSTER_LOG / "filter_transcriptome_by_nh_{sample}.log",
         nh=config["nh"],
@@ -618,9 +619,9 @@ rule filter_transcriptome_by_nh:
 
 rule remove_header_genome_mappings:
     input:
-        gmap=OUT_DIR / "{sample}" / "genome_mappings_filtered_nh.sam",
+        gmap=INTERMEDIATES_DIR / "{sample}" / "genome_mappings_filtered_nh.sam",
     output:
-        gmap=OUT_DIR / "{sample}" / "genome_mappings_no_header.sam",
+        gmap=INTERMEDIATES_DIR / "{sample}" / "genome_mappings_no_header.sam",
     params:
         cluster_log=CLUSTER_LOG / "remove_header_genome_mappings_{sample}.log",
     log:
@@ -640,9 +641,9 @@ rule remove_header_genome_mappings:
 
 rule remove_header_transcriptome_mappings:
     input:
-        tmap=OUT_DIR / "{sample}" / "transcriptome_mappings_filtered_nh.sam",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings_filtered_nh.sam",
     output:
-        tmap=OUT_DIR / "{sample}" / "transcriptome_mappings_no_header.sam",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings_no_header.sam",
     params:
         cluster_log=CLUSTER_LOG / "remove_header_transcriptome_mappings_{sample}.log",
     log:
@@ -662,11 +663,11 @@ rule remove_header_transcriptome_mappings:
 
 rule transcriptome_to_genome_maps:
     input:
-        tmap=OUT_DIR / "{sample}" / "transcriptome_mappings_no_header.sam",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings_no_header.sam",
         script=SCRIPTS_DIR / "sam_trx_to_sam_gen.pl",
-        exons=OUT_DIR / "exons.bed",
+        exons=INTERMEDIATES_DIR / "exons.bed",
     output:
-        genout=OUT_DIR / "{sample}" / "transcriptome_mappings_to_genome.sam",
+        genout=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings_to_genome.sam",
     params:
         cluster_log=CLUSTER_LOG / "transcriptome_to_genome_maps_{sample}.log",
     log:
@@ -690,10 +691,10 @@ rule transcriptome_to_genome_maps:
 
 rule merge_all_maps:
     input:
-        gmap1=OUT_DIR / "{sample}" / "transcriptome_mappings_to_genome.sam",
-        gmap2=OUT_DIR / "{sample}" / "genome_mappings_no_header.sam",
+        gmap1=INTERMEDIATES_DIR / "{sample}" / "transcriptome_mappings_to_genome.sam",
+        gmap2=INTERMEDIATES_DIR / "{sample}" / "genome_mappings_no_header.sam",
     output:
-        catmaps=OUT_DIR / "{sample}" / "mappings_all_no_header.sam",
+        catmaps=INTERMEDIATES_DIR / "{sample}" / "mappings_all_no_header.sam",
     params:
         cluster_log=CLUSTER_LOG / "merge_all_mappings_{sample}.log",
     log:
@@ -711,10 +712,10 @@ rule merge_all_maps:
 
 rule add_header_all_maps:
     input:
-        header=OUT_DIR / "genome_header.sam",
-        catmaps=OUT_DIR / "{sample}" / "mappings_all_no_header.sam",
+        header=INTERMEDIATES_DIR / "genome_header.sam",
+        catmaps=INTERMEDIATES_DIR / "{sample}" / "mappings_all_no_header.sam",
     output:
-        concatenate=OUT_DIR / "{sample}" / "mappings_all.sam",
+        concatenate=INTERMEDIATES_DIR / "{sample}" / "mappings_all.sam",
     params:
         cluster_log=CLUSTER_LOG / "add_header_{sample}.log",
     log:
@@ -732,9 +733,9 @@ rule add_header_all_maps:
 
 rule sort_maps_by_id:
     input:
-        concatenate=OUT_DIR / "{sample}" / "mappings_all.sam",
+        concatenate=INTERMEDIATES_DIR / "{sample}" / "mappings_all.sam",
     output:
-        sort=OUT_DIR / "{sample}" / "mappings_all_sorted_by_id.sam",
+        sort=INTERMEDIATES_DIR / "{sample}" / "mappings_all_sorted_by_id.sam",
     params:
         cluster_log=CLUSTER_LOG / "sort_maps_by_id_{sample}.log",
     log:
@@ -754,10 +755,10 @@ rule sort_maps_by_id:
 
 rule remove_inferiors:
     input:
-        sort=OUT_DIR / "{sample}" / "mappings_all_sorted_by_id.sam",
+        sort=INTERMEDIATES_DIR / "{sample}" / "mappings_all_sorted_by_id.sam",
         script=SCRIPTS_DIR / "sam_remove_duplicates_inferior_alignments_multimappers.pl",
     output:
-        remove_inf=OUT_DIR / "{sample}" / "mappings_all_removed_inferiors.sam",
+        remove_inf=INTERMEDIATES_DIR / "{sample}" / "mappings_all_removed_inferiors.sam",
     params:
         cluster_log=CLUSTER_LOG / "remove_inferiors_{sample}.log",
     log:
@@ -785,10 +786,10 @@ rule remove_inferiors:
 
 rule filter_by_indels:
     input:
-        sam=OUT_DIR / "{sample}" / "mappings_all_removed_inferiors.sam",
+        sam=INTERMEDIATES_DIR / "{sample}" / "mappings_all_removed_inferiors.sam",
         script=SCRIPTS_DIR / "filter_multimappers.py",
     output:
-        sam=OUT_DIR / "{sample}" / "alignments_all.sam",
+        sam=INTERMEDIATES_DIR / "{sample}" / "alignments_all.sam",
     params:
         cluster_log=CLUSTER_LOG / "remove_multimappers_{sample}.log",
     log:
@@ -815,9 +816,9 @@ rule filter_by_indels:
 
 rule convert_all_alns_sam_to_bam:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_all.sam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_all.sam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_all.bam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_all.bam",
     params:
         cluster_log=CLUSTER_LOG / "convert_all_alns_sam_to_bam_{sample}.log",
     log:
@@ -837,9 +838,9 @@ rule convert_all_alns_sam_to_bam:
 
 rule sort_all_alns_bam_by_position:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_all.bam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_all.bam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_all_sorted_{sample}.bam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_all_sorted_{sample}.bam",
     params:
         cluster_log=CLUSTER_LOG / "sort_all_alns_bam_by_position_{sample}.log",
     log:
@@ -859,9 +860,9 @@ rule sort_all_alns_bam_by_position:
 
 rule index_all_alns_bam:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_all_sorted.bam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_all_sorted.bam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_all_sorted.bam.bai",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_all_sorted.bam.bai",
     params:
         cluster_log=CLUSTER_LOG / "index_all_alns_bam_{sample}.log",
     log:
diff --git a/workflow/rules/prepare.smk b/workflow/rules/prepare.smk
index 0f98a4b..85d5625 100644
--- a/workflow/rules/prepare.smk
+++ b/workflow/rules/prepare.smk
@@ -26,7 +26,7 @@ validate(config, Path("../../config/config_schema.json"))
 
 
 ENV_DIR = Path(f"{workflow.basedir}/envs")
-OUT_DIR = Path(config["output_dir"])
+INTERMEDIATES_DIR = Path(config["intermediates_dir"])
 SCRIPTS_DIR = Path(config["scripts_dir"])
 
 CLUSTER_LOG = Path(config["cluster_log"])
@@ -49,17 +49,17 @@ localrules:
 
 rule finish_prepare:
     input:
-        idx_transcriptome=OUT_DIR / "segemehl_transcriptome_index.idx",
-        idx_genome=OUT_DIR / "segemehl_genome_index.idx",
-        exons=OUT_DIR / "exons.bed",
-        header=OUT_DIR / "genome_header.sam",
-        chrsize=OUT_DIR / "chr_size.txt",
+        idx_transcriptome=INTERMEDIATES_DIR / "segemehl_transcriptome_index.idx",
+        idx_genome=INTERMEDIATES_DIR / "segemehl_genome_index.idx",
+        exons=INTERMEDIATES_DIR / "exons.bed",
+        header=INTERMEDIATES_DIR / "genome_header.sam",
+        chrsize=INTERMEDIATES_DIR / "chr_size.txt",
         extended_mir=expand(
-            OUT_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
+            INTERMEDIATES_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
             extension=config["extension"],
         ),
         extended_primir=expand(
-            OUT_DIR / "extended_primir_annotation_{extension}_nt.gff3",
+            INTERMEDIATES_DIR / "extended_primir_annotation_{extension}_nt.gff3",
             extension=config["extension"],
         ),
 
@@ -74,7 +74,7 @@ rule trim_genome_seq_ids:
         genome=config["genome_file"],
         script=SCRIPTS_DIR / "trim_id_fasta.sh",
     output:
-        genome=OUT_DIR / "genome_processed.fa",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa",
     params:
         cluster_log=CLUSTER_LOG / "genome_process.log",
     log:
@@ -92,10 +92,10 @@ rule trim_genome_seq_ids:
 
 rule extract_transcriptome_seqs:
     input:
-        genome=OUT_DIR / "genome_processed.fa",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa",
         gtf=config["gtf_file"],
     output:
-        fasta=OUT_DIR / "transcriptome.fa",
+        fasta=INTERMEDIATES_DIR / "transcriptome.fa",
     params:
         cluster_log=CLUSTER_LOG / "extract_transcriptome_seqs.log",
     log:
@@ -115,10 +115,10 @@ rule extract_transcriptome_seqs:
 
 rule trim_transcriptome_seq_ids:
     input:
-        fasta=OUT_DIR / "transcriptome.fa",
+        fasta=INTERMEDIATES_DIR / "transcriptome.fa",
         script=SCRIPTS_DIR / "trim_id_fasta.sh",
     output:
-        fasta=OUT_DIR / "transcriptome_trimmed_id.fa",
+        fasta=INTERMEDIATES_DIR / "transcriptome_trimmed_id.fa",
     params:
         cluster_log=CLUSTER_LOG / "trim_transcriptome.log",
     log:
@@ -136,9 +136,9 @@ rule trim_transcriptome_seq_ids:
 
 rule generate_segemehl_index_transcriptome:
     input:
-        fasta=OUT_DIR / "transcriptome_trimmed_id.fa",
+        fasta=INTERMEDIATES_DIR / "transcriptome_trimmed_id.fa",
     output:
-        idx=OUT_DIR / "segemehl_transcriptome_index.idx",
+        idx=INTERMEDIATES_DIR / "segemehl_transcriptome_index.idx",
     params:
         cluster_log=CLUSTER_LOG / "generate_segemehl_index_transcriptome.log",
     log:
@@ -162,9 +162,9 @@ rule generate_segemehl_index_transcriptome:
 
 rule generate_segemehl_index_genome:
     input:
-        genome=OUT_DIR / "genome_processed.fa",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa",
     output:
-        idx=OUT_DIR / "segemehl_genome_index.idx",
+        idx=INTERMEDIATES_DIR / "segemehl_genome_index.idx",
     params:
         cluster_log=CLUSTER_LOG / "generate_segemehl_index_genome.log",
     log:
@@ -191,7 +191,7 @@ rule get_exons_gtf:
         gtf=config["gtf_file"],
         script=SCRIPTS_DIR / "get_lines_w_pattern.sh",
     output:
-        exons=OUT_DIR / "exons.gtf",
+        exons=INTERMEDIATES_DIR / "exons.gtf",
     params:
         cluster_log=CLUSTER_LOG / "get_exons_gtf.log",
     log:
@@ -215,10 +215,10 @@ rule get_exons_gtf:
 
 rule convert_exons_gtf_to_bed:
     input:
-        exons=OUT_DIR / "exons.gtf",
+        exons=INTERMEDIATES_DIR / "exons.gtf",
         script=SCRIPTS_DIR / "gtf_exons_bed.1.1.2.R",
     output:
-        exons=OUT_DIR / "exons.bed",
+        exons=INTERMEDIATES_DIR / "exons.bed",
     params:
         cluster_log=CLUSTER_LOG / "exons_gtf_to_bed.log",
     log:
@@ -242,9 +242,9 @@ rule convert_exons_gtf_to_bed:
 
 rule create_genome_header:
     input:
-        genome=OUT_DIR / "genome_processed.fa",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa",
     output:
-        header=OUT_DIR / "genome_header.sam",
+        header=INTERMEDIATES_DIR / "genome_header.sam",
     params:
         cluster_log=CLUSTER_LOG / "create_genome_header.log",
     log:
@@ -268,7 +268,7 @@ rule map_chr_names:
         script=SCRIPTS_DIR / "map_chromosomes.pl",
         map_chr=config["map_chr_file"],
     output:
-        gff=OUT_DIR / "mirna_annotations.gff3",
+        gff=INTERMEDIATES_DIR / "mirna_annotations.gff3",
     params:
         cluster_log=CLUSTER_LOG / "map_chr_names.log",
         column="1",
@@ -296,9 +296,9 @@ rule map_chr_names:
 
 rule create_index_genome_fasta:
     input:
-        genome=OUT_DIR / "genome_processed.fa",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa",
     output:
-        genome=OUT_DIR / "genome_processed.fa.fai",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa.fai",
     params:
         cluster_log=CLUSTER_LOG / "create_index_genome_fasta.log",
     log:
@@ -318,9 +318,9 @@ rule create_index_genome_fasta:
 
 rule extract_chr_len:
     input:
-        genome=OUT_DIR / "genome_processed.fa.fai",
+        genome=INTERMEDIATES_DIR / "genome_processed.fa.fai",
     output:
-        chrsize=OUT_DIR / "chr_size.txt",
+        chrsize=INTERMEDIATES_DIR / "chr_size.txt",
     params:
         cluster_log=CLUSTER_LOG / "extract_chr_len.log",
     log:
@@ -338,21 +338,21 @@ rule extract_chr_len:
 
 rule extend_mirs_annotations:
     input:
-        gff3=OUT_DIR / "mirna_annotations.gff3",
-        chrsize=OUT_DIR / "chr_size.txt",
+        gff3=INTERMEDIATES_DIR / "mirna_annotations.gff3",
+        chrsize=INTERMEDIATES_DIR / "chr_size.txt",
         script=SCRIPTS_DIR / "mirna_extension.py",
     output:
         extended_mir=expand(
-            OUT_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
+            INTERMEDIATES_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
             extension=config["extension"],
         ),
         extended_primir=expand(
-            OUT_DIR / "extended_primir_annotation_{extension}_nt.gff3",
+            INTERMEDIATES_DIR / "extended_primir_annotation_{extension}_nt.gff3",
             extension=config["extension"],
         ),
     params:
         cluster_log=CLUSTER_LOG / "extend_mirs_annotations.log",
-        out_dir=OUT_DIR,
+        out_dir=INTERMEDIATES_DIR,
         extension=config["extension"],
     log:
         LOCAL_LOG / "extend_mirs_annotations.log",
diff --git a/workflow/rules/quantify.smk b/workflow/rules/quantify.smk
index 15aa1e7..e3fe767 100644
--- a/workflow/rules/quantify.smk
+++ b/workflow/rules/quantify.smk
@@ -25,6 +25,7 @@ validate(config, Path("../../config/config_schema.json"))
 
 ENV_DIR = Path(f"{workflow.basedir}/envs")
 OUT_DIR = Path(config["output_dir"])
+INTERMEDIATES_DIR = Path(config["intermediates_dir"])
 SCRIPTS_DIR = Path(config["scripts_dir"])
 
 CLUSTER_LOG = Path(config["cluster_log"])
@@ -63,9 +64,6 @@ rule finish_quantify:
     input:
         primir_intersect_sam=OUT_DIR / "{sample}" / "alignments_intersecting_primir.sam",
         mirna_intersect_sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
-        intersect_sam=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_sorted_tag.sam",
         table=OUT_DIR / "TABLES" / "all_{mir}_counts.tab",
         uncollapsed_bam=expand(
             OUT_DIR
@@ -88,13 +86,13 @@ rule finish_quantify:
 
 rule intersect_extended_primir:
     input:
-        alignment=OUT_DIR / "{sample}" / "alignments_all_sorted_{sample}.bam",
+        alignment=INTERMEDIATES_DIR / "{sample}" / "alignments_all_sorted_{sample}.bam",
         primir=expand(
-            OUT_DIR / "extended_primir_annotation_{extension}_nt.gff3",
+            INTERMEDIATES_DIR / "extended_primir_annotation_{extension}_nt.gff3",
             extension=config["extension"],
         ),
     output:
-        intersect=OUT_DIR / "{sample}" / "intersected_extended_primir.bed",
+        intersect=INTERMEDIATES_DIR / "{sample}" / "intersected_extended_primir.bed",
     params:
         cluster_log=CLUSTER_LOG / "intersect_extended_primir_{sample}.log",
     log:
@@ -122,8 +120,8 @@ rule intersect_extended_primir:
 
 rule filter_sam_by_intersecting_primir:
     input:
-        alignments=OUT_DIR / "{sample}" / "alignments_all.sam",
-        intersect=OUT_DIR / "{sample}" / "intersected_extended_primir.bed",
+        alignments=INTERMEDIATES_DIR / "{sample}" / "alignments_all.sam",
+        intersect=INTERMEDIATES_DIR / "{sample}" / "intersected_extended_primir.bed",
     output:
         sam=OUT_DIR / "{sample}" / "alignments_intersecting_primir.sam",
     params:
@@ -152,7 +150,7 @@ rule convert_intersecting_primir_sam_to_bam:
     input:
         maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir.sam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir.bam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_intersecting_primir.bam",
     params:
         cluster_log=CLUSTER_LOG / "convert_intersecting_primir_sam_to_bam_{sample}.log",
     log:
@@ -172,9 +170,11 @@ rule convert_intersecting_primir_sam_to_bam:
 
 rule sort_intersecting_primir_bam_by_position:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir.bam",
+        maps=INTERMEDIATES_DIR / "{sample}" / "alignments_intersecting_primir.bam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_primir_sorted.bam",
     params:
         cluster_log=CLUSTER_LOG
         / "sort_intersecting_primir_bam_by_position_{sample}.log",
@@ -195,9 +195,13 @@ rule sort_intersecting_primir_bam_by_position:
 
 rule index_intersecting_primir_bam:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_primir_sorted.bam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam.bai",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_primir_sorted.bam.bai",
     params:
         cluster_log=CLUSTER_LOG / "index_intersecting_primir_bam_{sample}.log",
     log:
@@ -217,13 +221,15 @@ rule index_intersecting_primir_bam:
 
 rule intersect_extended_mirna:
     input:
-        alignment=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam",
+        alignment=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_primir_sorted.bam",
         mirna=expand(
-            OUT_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
+            INTERMEDIATES_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
             extension=config["extension"],
         ),
     output:
-        intersect=OUT_DIR / "{sample}" / "intersected_extended_mirna.bed",
+        intersect=INTERMEDIATES_DIR / "{sample}" / "intersected_extended_mirna.bed",
     params:
         cluster_log=CLUSTER_LOG / "intersect_extended_mirna_{sample}.log",
     log:
@@ -252,7 +258,7 @@ rule intersect_extended_mirna:
 rule filter_sam_by_intersecting_mirna:
     input:
         alignments=OUT_DIR / "{sample}" / "alignments_intersecting_primir.sam",
-        intersect=OUT_DIR / "{sample}" / "intersected_extended_mirna.bed",
+        intersect=INTERMEDIATES_DIR / "{sample}" / "intersected_extended_mirna.bed",
     output:
         sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
     params:
@@ -280,10 +286,10 @@ rule filter_sam_by_intersecting_mirna:
 rule add_intersecting_mirna_tag:
     input:
         alignments=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
-        intersect=OUT_DIR / "{sample}" / "intersected_extended_mirna.bed",
+        intersect=INTERMEDIATES_DIR / "{sample}" / "intersected_extended_mirna.bed",
         script=SCRIPTS_DIR / "iso_name_tagging.py",
     output:
-        sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_tag.sam",
+        sam=INTERMEDIATES_DIR / "{sample}" / "alignments_intersecting_mirna_tag.sam",
     params:
         extension=config["extension"],
         cluster_log=CLUSTER_LOG / "add_intersecting_mirna_tag_{sample}.log",
@@ -309,9 +315,11 @@ rule add_intersecting_mirna_tag:
 
 rule sort_intersecting_mirna_by_feat_tag:
     input:
-        sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_tag.sam",
+        sam=INTERMEDIATES_DIR / "{sample}" / "alignments_intersecting_mirna_tag.sam",
     output:
-        sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_sorted_tag.sam",
+        sam=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_mirna_sorted_tag.sam",
     params:
         cluster_log=CLUSTER_LOG / "sort_intersecting_mirna_by_feat_tag_{sample}.log",
     log:
@@ -331,15 +339,17 @@ rule sort_intersecting_mirna_by_feat_tag:
 
 rule quantify_mirna:
     input:
-        alignments=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_sorted_tag.sam",
+        alignments=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_mirna_sorted_tag.sam",
         script=SCRIPTS_DIR / "mirna_quantification.py",
     output:
-        table=OUT_DIR / "TABLES" / "mirna_counts_{sample}",
+        table=INTERMEDIATES_DIR / "TABLES" / "mirna_counts_{sample}",
     params:
         cluster_log=CLUSTER_LOG / "quantify_mirna_{sample}.log",
         mir_list=config["mir_list"],
         library="{sample}",
-        out_dir=OUT_DIR / "TABLES",
+        out_dir=INTERMEDIATES_DIR / "TABLES",
     log:
         LOCAL_LOG / "quantify_mirna_{sample}.log",
     container:
@@ -365,10 +375,10 @@ rule quantify_mirna:
 
 rule quantify_primir:
     input:
-        intersect=OUT_DIR / "{sample}" / "intersected_extended_primir.bed",
+        intersect=INTERMEDIATES_DIR / "{sample}" / "intersected_extended_primir.bed",
         script=SCRIPTS_DIR / "primir_quantification.py",
     output:
-        table=OUT_DIR / "TABLES" / "pri-mir_counts_{sample}",
+        table=INTERMEDIATES_DIR / "TABLES" / "pri-mir_counts_{sample}",
     params:
         cluster_log=CLUSTER_LOG / "quantify_primir_{sample}.log",
     log:
@@ -395,7 +405,7 @@ rule quantify_primir:
 rule merge_tables:
     input:
         table=expand(
-            OUT_DIR / "TABLES" / "{mir}_counts_{sample}",
+            INTERMEDIATES_DIR / "TABLES" / "{mir}_counts_{sample}",
             sample=pd.unique(samples_table.index.values),
             mir=[mir for mir in config["mir_list"] if mir != "isomir"],
         ),
@@ -405,7 +415,7 @@ rule merge_tables:
     params:
         cluster_log=CLUSTER_LOG / "merge_tables_{mirna}.log",
         prefix="{mirna}_counts_",
-        input_dir=OUT_DIR / "TABLES",
+        input_dir=INTERMEDIATES_DIR / "TABLES",
     log:
         LOCAL_LOG / "merge_tables_{mirna}.log",
     container:
@@ -432,7 +442,9 @@ rule uncollapse_reads:
         maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
         script=SCRIPTS_DIR / "sam_uncollapse.pl",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.sam",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_mirna_uncollapsed.sam",
     params:
         cluster_log=CLUSTER_LOG / "uncollapse_reads_{sample}.log",
     log:
@@ -456,9 +468,13 @@ rule uncollapse_reads:
 
 rule convert_uncollpased_reads_sam_to_bam:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.sam",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_mirna_uncollapsed.sam",
     output:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.bam",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_mirna_uncollapsed.bam",
     params:
         cluster_log=CLUSTER_LOG / "convert_uncollapsed_reads_sam_to_bam_{sample}.log",
     log:
@@ -478,7 +494,9 @@ rule convert_uncollpased_reads_sam_to_bam:
 
 rule sort_uncollpased_reads_bam_by_position:
     input:
-        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.bam",
+        maps=INTERMEDIATES_DIR
+        / "{sample}"
+        / "alignments_intersecting_mirna_uncollapsed.bam",
     output:
         maps=OUT_DIR
         / "{sample}"