diff --git a/README.md b/README.md
index c4c32929964c49cd58de998e23f2e78fd1555ea6..1946224ad882feebf9ce80cfda45338f815cb3a9 100644
--- a/README.md
+++ b/README.md
@@ -5,13 +5,16 @@ developed by the [Zavolan lab][zavolan-lab].
 
 Reads are processed, aligned, quantified and analyzed with state-of-the-art
 tools to give meaningful initial insights into various aspects of an RNA-Seq
-library while cutting down on hands-on time for bioinformaticians. For a more detailed description of the individual rules please refer to the [pipeline documentation][pipeline-documentation].    
+library while cutting down on hands-on time for bioinformaticians.
 
-Below is a visual representation of the individual workflow steps ("pe"
+Below is a schematic representation of the individual workflow steps ("pe"
 refers to "paired-end"):
 
 > ![rule_graph][rule-graph]
 
+For a more detailed description of each step, please refer to the [pipeline
+documentation][pipeline-documentation].
+
 ## Requirements
 
 Currently the workflow is only available for Linux distributions. It was tested
@@ -329,4 +332,4 @@ Contaminant sequences | contaminant_seqs
 [singularity-install]: <https://sylabs.io/guides/3.5/admin-guide/installation.html>
 [slurm]: <https://slurm.schedmd.com/documentation.html>
 [zavolan-lab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>
-[pipeline-documentation]: pipeline_documentation.md
\ No newline at end of file
+[pipeline-documentation]: pipeline_documentation.md
diff --git a/Snakefile b/Snakefile
index 9876c7270bea945765a191363799899409f36790..f71135ad47e7f42837e9e1c052403f55cc9eb36a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -147,7 +147,7 @@ rule extract_transcriptome:
             config['log_dir'],
             "{organism}_extract_transcriptome.log")
     singularity:
-        "docker://zavolab/gffread:0.11.7"
+        "docker://zavolab/gffread:0.11.7-slim"
     shell:
         "(gffread \
         -w {output.transcriptome} \
@@ -743,7 +743,7 @@ rule generate_alfa_index:
     threads: 4
 
     singularity: 
-        "docker://zavolab/alfa:1.1.1"
+        "docker://zavolab/alfa:1.1.1-slim"
 
     log: 
         os.path.join(config["log_dir"], "{organism}_{index_size}_generate_alfa_index.log")
@@ -813,7 +813,7 @@ rule alfa_qc:
         name = "{sample}"
 
     singularity:
-        "docker://zavolab/alfa:1.1.1"
+        "docker://zavolab/alfa:1.1.1-slim"
 
     log: 
         os.path.abspath(os.path.join(
@@ -864,7 +864,7 @@ rule alfa_qc_all_samples:
             "alfa_qc_all_samples.{unique}.log"))
 
     singularity:
-        "docker://zavolab/alfa:1.1.1"
+        "docker://zavolab/alfa:1.1.1-slim"
 
     shell:
         """
@@ -897,7 +897,7 @@ rule alfa_concat_results:
             "alfa_qc_all_samples.concat.log"))
 
     singularity:
-        "docker://zavolab/imagemagick:7.0.8"
+        "docker://zavolab/imagemagick:6.9.10-slim"
 
     shell:
         """
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 5a911b610ed2ee233d7c99bfce825c8a259415ba..b4b01ad87a12f4402b29785187728907d9546541 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,740 +1,740 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
  -->
 <!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 2395.00 913.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+ viewBox="0.00 0.00 2395.06 913.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 909)">
 <title>snakemake_dag</title>
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+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-909 2391.0607,-909 2391.0607,4 -4,4"/>
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 <g id="node1" class="node">
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 <g id="node2" class="node">
 <title>1</title>
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-<text text-anchor="middle" x="1272.5" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
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-<text text-anchor="middle" x="1272.5" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
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+<text text-anchor="middle" x="1272.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_MultiQC_config</text>
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-<text text-anchor="middle" x="1272.5" y="-226" font-family="sans" font-size="10.00">output_dir: results</text>
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 <g id="node5" class="node">
 <title>4</title>
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-<text text-anchor="middle" x="162.5" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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+<text text-anchor="middle" x="162.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
+<text text-anchor="middle" x="162.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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 <g id="node6" class="node">
 <title>5</title>
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+<text text-anchor="middle" x="1326.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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 <title>8</title>
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+<text text-anchor="middle" x="1478.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
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 <g id="node10" class="node">
 <title>9</title>
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-<text text-anchor="middle" x="1004.5" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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+<text text-anchor="middle" x="1004.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
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 <!-- 9&#45;&gt;3 -->
 <g id="edge9" class="edge">
 <title>9&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1198.2,-258.02 1206.99,-252.11 1196.43,-251.25 1198.2,-258.02"/>
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 <!-- 10 -->
 <g id="node11" class="node">
 <title>10</title>
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-<text text-anchor="middle" x="1179.5" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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+<text text-anchor="middle" x="1179.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
 </g>
 <!-- 10&#45;&gt;3 -->
 <g id="edge10" class="edge">
 <title>10&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1243.89,-260.91 1249.78,-252.1 1239.68,-255.32 1243.89,-260.91"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1202.9678,-287.8314C1214.5327,-278.8779 1228.6404,-267.9558 1241.1183,-258.2955"/>
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 <!-- 11 -->
 <g id="node12" class="node">
 <title>11</title>
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-<text text-anchor="middle" x="1365.5" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1365.5" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M1440.5,-324C1440.5,-324 1290.5,-324 1290.5,-324 1284.5,-324 1278.5,-318 1278.5,-312 1278.5,-312 1278.5,-300 1278.5,-300 1278.5,-294 1284.5,-288 1290.5,-288 1290.5,-288 1440.5,-288 1440.5,-288 1446.5,-288 1452.5,-294 1452.5,-300 1452.5,-300 1452.5,-312 1452.5,-312 1452.5,-318 1446.5,-324 1440.5,-324"/>
+<text text-anchor="middle" x="1365.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1365.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
 </g>
 <!-- 11&#45;&gt;3 -->
 <g id="edge11" class="edge">
 <title>11&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1305.32,-255.32 1295.22,-252.1 1301.11,-260.91 1305.32,-255.32"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1342.0322,-287.8314C1330.4673,-278.8779 1316.3596,-267.9558 1303.8817,-258.2955"/>
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 <!-- 12 -->
 <g id="node13" class="node">
 <title>12</title>
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-<text text-anchor="middle" x="823.5" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="823.5" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M898.5,-324C898.5,-324 748.5,-324 748.5,-324 742.5,-324 736.5,-318 736.5,-312 736.5,-312 736.5,-300 736.5,-300 736.5,-294 742.5,-288 748.5,-288 748.5,-288 898.5,-288 898.5,-288 904.5,-288 910.5,-294 910.5,-300 910.5,-300 910.5,-312 910.5,-312 910.5,-318 904.5,-324 898.5,-324"/>
+<text text-anchor="middle" x="823.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="823.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
 </g>
 <!-- 12&#45;&gt;3 -->
 <g id="edge12" class="edge">
 <title>12&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1196.33,-249.38 1205.73,-244.49 1195.33,-242.46 1196.33,-249.38"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M910.5981,-289.5372C913.6005,-289.0118 916.5746,-288.4979 919.5,-288 1014.3082,-271.8648 1123.8293,-255.4566 1195.4227,-245.0306"/>
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 <g id="node14" class="node">
 <title>13</title>
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-<text text-anchor="middle" x="1714.5" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1732.5,-612C1732.5,-612 1696.5,-612 1696.5,-612 1690.5,-612 1684.5,-606 1684.5,-600 1684.5,-600 1684.5,-588 1684.5,-588 1684.5,-582 1690.5,-576 1696.5,-576 1696.5,-576 1732.5,-576 1732.5,-576 1738.5,-576 1744.5,-582 1744.5,-588 1744.5,-588 1744.5,-600 1744.5,-600 1744.5,-606 1738.5,-612 1732.5,-612"/>
+<text text-anchor="middle" x="1714.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
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 <!-- 13&#45;&gt;3 -->
 <g id="edge13" class="edge">
 <title>13&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.44,-237.36 1339.09,-239.59 1348.58,-244.3 1349.44,-237.36"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1684.3802,-579.7846C1681.3949,-578.4704 1678.398,-577.1878 1675.5,-576 1631.7921,-558.0856 1606.528,-575.617 1575.5,-540 1548.6464,-509.1748 1556.5,-490.8816 1556.5,-450 1556.5,-450 1556.5,-450 1556.5,-378 1556.5,-284.7709 1433.2511,-251.882 1349.1381,-240.2921"/>
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 <!-- 40 -->
 <g id="node41" class="node">
 <title>40</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M1882.5,-540C1882.5,-540 1760.5,-540 1760.5,-540 1754.5,-540 1748.5,-534 1748.5,-528 1748.5,-528 1748.5,-516 1748.5,-516 1748.5,-510 1754.5,-504 1760.5,-504 1760.5,-504 1882.5,-504 1882.5,-504 1888.5,-504 1894.5,-510 1894.5,-516 1894.5,-516 1894.5,-528 1894.5,-528 1894.5,-534 1888.5,-540 1882.5,-540"/>
-<text text-anchor="middle" x="1821.5" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1821.5" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1882.5,-540C1882.5,-540 1760.5,-540 1760.5,-540 1754.5,-540 1748.5,-534 1748.5,-528 1748.5,-528 1748.5,-516 1748.5,-516 1748.5,-510 1754.5,-504 1760.5,-504 1760.5,-504 1882.5,-504 1882.5,-504 1888.5,-504 1894.5,-510 1894.5,-516 1894.5,-516 1894.5,-528 1894.5,-528 1894.5,-534 1888.5,-540 1882.5,-540"/>
+<text text-anchor="middle" x="1821.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1821.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
 </g>
 <!-- 13&#45;&gt;40 -->
 <g id="edge69" class="edge">
 <title>13&#45;&gt;40</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1788.77,-548.59 1795.22,-540.19 1784.94,-542.74 1788.77,-548.59"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1741.5006,-575.8314C1754.9331,-566.7927 1771.3473,-555.7476 1785.8039,-546.0198"/>
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 <!-- 43 -->
 <g id="node44" class="node">
 <title>43</title>
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-<text text-anchor="middle" x="1657.5" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1718.5,-540C1718.5,-540 1596.5,-540 1596.5,-540 1590.5,-540 1584.5,-534 1584.5,-528 1584.5,-528 1584.5,-516 1584.5,-516 1584.5,-510 1590.5,-504 1596.5,-504 1596.5,-504 1718.5,-504 1718.5,-504 1724.5,-504 1730.5,-510 1730.5,-516 1730.5,-516 1730.5,-528 1730.5,-528 1730.5,-534 1724.5,-540 1718.5,-540"/>
+<text text-anchor="middle" x="1657.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
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 </g>
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 <g id="edge72" class="edge">
 <title>13&#45;&gt;43</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1680.46,-545.65 1671.43,-540.1 1675.03,-550.07 1680.46,-545.65"/>
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 <g id="node15" class="node">
 <title>14</title>
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-<text text-anchor="middle" x="2076.5" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
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 <title>14&#45;&gt;3</title>
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 <g id="node43" class="node">
 <title>42</title>
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 <g id="edge71" class="edge">
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 <g id="node45" class="node">
 <title>44</title>
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-<text text-anchor="middle" x="1985.5" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M2046.5,-540C2046.5,-540 1924.5,-540 1924.5,-540 1918.5,-540 1912.5,-534 1912.5,-528 1912.5,-528 1912.5,-516 1912.5,-516 1912.5,-510 1918.5,-504 1924.5,-504 1924.5,-504 2046.5,-504 2046.5,-504 2052.5,-504 2058.5,-510 2058.5,-516 2058.5,-516 2058.5,-528 2058.5,-528 2058.5,-534 2052.5,-540 2046.5,-540"/>
+<text text-anchor="middle" x="1985.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1985.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
 </g>
 <!-- 14&#45;&gt;44 -->
 <g id="edge73" class="edge">
 <title>14&#45;&gt;44</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="2017.8,-543.43 2007.74,-540.1 2013.53,-548.98 2017.8,-543.43"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2053.5369,-575.8314C2042.3285,-566.9632 2028.6791,-556.1637 2016.5561,-546.5718"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2018.4697,-543.6229 2008.4558,-540.1628 2014.1263,-549.1125 2018.4697,-543.6229"/>
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 <!-- 15 -->
 <g id="node16" class="node">
 <title>15</title>
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-<text text-anchor="middle" x="1848.5" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1892,-324C1892,-324 1805,-324 1805,-324 1799,-324 1793,-318 1793,-312 1793,-312 1793,-300 1793,-300 1793,-294 1799,-288 1805,-288 1805,-288 1892,-288 1892,-288 1898,-288 1904,-294 1904,-300 1904,-300 1904,-312 1904,-312 1904,-318 1898,-324 1892,-324"/>
+<text text-anchor="middle" x="1848.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
 </g>
 <!-- 15&#45;&gt;3 -->
 <g id="edge15" class="edge">
 <title>15&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.63,-240.85 1339.28,-243.12 1348.78,-247.8 1349.63,-240.85"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1792.7473,-299.0309C1689.1854,-286.0857 1466.9881,-258.311 1349.2964,-243.5996"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1349.6346,-240.1147 1339.2776,-242.3472 1348.7663,-247.0606 1349.6346,-240.1147"/>
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 <!-- 16 -->
 <g id="node17" class="node">
 <title>16</title>
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-<text text-anchor="middle" x="968.5" y="-810" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1032.5,-830.5C1032.5,-830.5 904.5,-830.5 904.5,-830.5 898.5,-830.5 892.5,-824.5 892.5,-818.5 892.5,-818.5 892.5,-806.5 892.5,-806.5 892.5,-800.5 898.5,-794.5 904.5,-794.5 904.5,-794.5 1032.5,-794.5 1032.5,-794.5 1038.5,-794.5 1044.5,-800.5 1044.5,-806.5 1044.5,-806.5 1044.5,-818.5 1044.5,-818.5 1044.5,-824.5 1038.5,-830.5 1032.5,-830.5"/>
+<text text-anchor="middle" x="968.5" y="-810" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
 </g>
 <!-- 16&#45;&gt;6 -->
 <g id="edge16" class="edge">
 <title>16&#45;&gt;6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M949.62,-794.37C924.03,-769.18 881.5,-719.42 881.5,-667 881.5,-667 881.5,-667 881.5,-521 881.5,-477.91 858.9,-432.26 842.42,-404.7"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="845.33,-402.75 837.1,-396.07 839.37,-406.42 845.33,-402.75"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M948.7584,-794.2151C923.0897,-768.348 881.5,-718.3581 881.5,-666 881.5,-666 881.5,-666 881.5,-522 881.5,-478.8617 859.4001,-433.0945 842.9668,-405.0255"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="845.8137,-402.9688 837.6512,-396.2143 839.82,-406.5847 845.8137,-402.9688"/>
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 <!-- 20 -->
 <g id="node21" class="node">
 <title>20</title>
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-<text text-anchor="middle" x="1008.5" y="-375.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1067.5,-396C1067.5,-396 949.5,-396 949.5,-396 943.5,-396 937.5,-390 937.5,-384 937.5,-384 937.5,-372 937.5,-372 937.5,-366 943.5,-360 949.5,-360 949.5,-360 1067.5,-360 1067.5,-360 1073.5,-360 1079.5,-366 1079.5,-372 1079.5,-372 1079.5,-384 1079.5,-384 1079.5,-390 1073.5,-396 1067.5,-396"/>
+<text text-anchor="middle" x="1008.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
 </g>
 <!-- 16&#45;&gt;20 -->
 <g id="edge40" class="edge">
 <title>16&#45;&gt;20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M968.5,-794.15C968.5,-767.02 968.5,-712.91 968.5,-667 968.5,-667 968.5,-667 968.5,-521 968.5,-479.48 984.54,-433.61 996.3,-405.54"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="999.65,-406.62 1000.41,-396.05 993.23,-403.84 999.65,-406.62"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M968.5,-794.4571C968.5,-766.8072 968.5,-712.2899 968.5,-666 968.5,-666 968.5,-666 968.5,-522 968.5,-480.2219 984.324,-434.0316 996.0664,-405.5067"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="999.3354,-406.7629 1000.017,-396.19 992.8908,-404.0301 999.3354,-406.7629"/>
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 <!-- 22 -->
 <g id="node23" class="node">
 <title>22</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1716,-756C1716,-756 1615,-756 1615,-756 1609,-756 1603,-750 1603,-744 1603,-744 1603,-732 1603,-732 1603,-726 1609,-720 1615,-720 1615,-720 1716,-720 1716,-720 1722,-720 1728,-726 1728,-732 1728,-732 1728,-744 1728,-744 1728,-750 1722,-756 1716,-756"/>
-<text text-anchor="middle" x="1665.5" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1716,-756C1716,-756 1615,-756 1615,-756 1609,-756 1603,-750 1603,-744 1603,-744 1603,-732 1603,-732 1603,-726 1609,-720 1615,-720 1615,-720 1716,-720 1716,-720 1722,-720 1728,-726 1728,-732 1728,-732 1728,-744 1728,-744 1728,-750 1722,-756 1716,-756"/>
+<text text-anchor="middle" x="1665.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
 </g>
 <!-- 16&#45;&gt;22 -->
 <g id="edge45" class="edge">
 <title>16&#45;&gt;22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1044.75,-803.57C1180.05,-789.5 1460.31,-760.34 1592.93,-746.55"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1593.4,-750.02 1602.99,-745.5 1592.68,-743.06 1593.4,-750.02"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1044.7512,-804.3498C1180.0467,-789.8885 1460.31,-759.9321 1592.9272,-745.7571"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1593.4149,-749.225 1602.9863,-744.6819 1592.6709,-742.2646 1593.4149,-749.225"/>
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 <!-- 17 -->
 <g id="node18" class="node">
 <title>17</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1245,-468C1245,-468 1148,-468 1148,-468 1142,-468 1136,-462 1136,-456 1136,-456 1136,-444 1136,-444 1136,-438 1142,-432 1148,-432 1148,-432 1245,-432 1245,-432 1251,-432 1257,-438 1257,-444 1257,-444 1257,-456 1257,-456 1257,-462 1251,-468 1245,-468"/>
-<text text-anchor="middle" x="1196.5" y="-447.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M1245,-468C1245,-468 1148,-468 1148,-468 1142,-468 1136,-462 1136,-456 1136,-456 1136,-444 1136,-444 1136,-438 1142,-432 1148,-432 1148,-432 1245,-432 1245,-432 1251,-432 1257,-438 1257,-444 1257,-444 1257,-456 1257,-456 1257,-462 1251,-468 1245,-468"/>
+<text text-anchor="middle" x="1196.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
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 <!-- 17&#45;&gt;6 -->
 <g id="edge17" class="edge">
 <title>17&#45;&gt;6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1135.85,-434.02C1132.69,-433.32 1129.56,-432.64 1126.5,-432 1089.55,-424.27 1000.66,-408.75 929.01,-396.5"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="929.46,-393.03 919.02,-394.79 928.28,-399.93 929.46,-393.03"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1135.8593,-434.1133C1132.6991,-433.3773 1129.5651,-432.6681 1126.5,-432 1107.1924,-427.7918 1008.5364,-410.2141 929.3559,-396.241"/>
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 <g id="edge19" class="edge">
 <title>17&#45;&gt;7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1228.3,-431.88C1245.61,-422.55 1267.22,-410.92 1285.76,-400.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1287.43,-404.01 1294.58,-396.19 1284.11,-397.85 1287.43,-404.01"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1229.3045,-431.8314C1246.0862,-422.5368 1266.6985,-411.1208 1284.6163,-401.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1286.6538,-404.0696 1293.706,-396.1628 1283.2623,-397.9461 1286.6538,-404.0696"/>
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 <!-- 18 -->
 <g id="node19" class="node">
 <title>18</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1378.5,-830.5C1378.5,-830.5 1268.5,-830.5 1268.5,-830.5 1262.5,-830.5 1256.5,-824.5 1256.5,-818.5 1256.5,-818.5 1256.5,-806.5 1256.5,-806.5 1256.5,-800.5 1262.5,-794.5 1268.5,-794.5 1268.5,-794.5 1378.5,-794.5 1378.5,-794.5 1384.5,-794.5 1390.5,-800.5 1390.5,-806.5 1390.5,-806.5 1390.5,-818.5 1390.5,-818.5 1390.5,-824.5 1384.5,-830.5 1378.5,-830.5"/>
-<text text-anchor="middle" x="1323.5" y="-810" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1378.5,-830.5C1378.5,-830.5 1268.5,-830.5 1268.5,-830.5 1262.5,-830.5 1256.5,-824.5 1256.5,-818.5 1256.5,-818.5 1256.5,-806.5 1256.5,-806.5 1256.5,-800.5 1262.5,-794.5 1268.5,-794.5 1268.5,-794.5 1378.5,-794.5 1378.5,-794.5 1384.5,-794.5 1390.5,-800.5 1390.5,-806.5 1390.5,-806.5 1390.5,-818.5 1390.5,-818.5 1390.5,-824.5 1384.5,-830.5 1378.5,-830.5"/>
+<text text-anchor="middle" x="1323.5" y="-810" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
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 <!-- 18&#45;&gt;7 -->
 <g id="edge18" class="edge">
 <title>18&#45;&gt;7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1323.5,-794.15C1323.5,-767.02 1323.5,-712.91 1323.5,-667 1323.5,-667 1323.5,-667 1323.5,-521 1323.5,-480.99 1324.71,-434.65 1325.59,-406.08"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1329.09,-406.15 1325.91,-396.05 1322.09,-405.93 1329.09,-406.15"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1323.5,-794.4571C1323.5,-766.8072 1323.5,-712.2899 1323.5,-666 1323.5,-666 1323.5,-666 1323.5,-522 1323.5,-481.8673 1324.6792,-435.4566 1325.5589,-406.414"/>
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 <g id="node22" class="node">
 <title>21</title>
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-<text text-anchor="middle" x="1160.5" y="-375.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1211,-396C1211,-396 1110,-396 1110,-396 1104,-396 1098,-390 1098,-384 1098,-384 1098,-372 1098,-372 1098,-366 1104,-360 1110,-360 1110,-360 1211,-360 1211,-360 1217,-360 1223,-366 1223,-372 1223,-372 1223,-384 1223,-384 1223,-390 1217,-396 1211,-396"/>
+<text text-anchor="middle" x="1160.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
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 <g id="edge42" class="edge">
 <title>18&#45;&gt;21</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1315.6264,-794.3912C1304.4959,-767.101 1285.5,-713.559 1285.5,-666 1285.5,-666 1285.5,-666 1285.5,-522 1285.5,-481.1184 1291.3659,-464.4499 1266.5,-432 1256.3571,-418.7635 1242.0678,-408.5049 1227.2566,-400.6623"/>
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 <g id="node25" class="node">
 <title>24</title>
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-<text text-anchor="middle" x="1877.5" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M1919,-756C1919,-756 1836,-756 1836,-756 1830,-756 1824,-750 1824,-744 1824,-744 1824,-732 1824,-732 1824,-726 1830,-720 1836,-720 1836,-720 1919,-720 1919,-720 1925,-720 1931,-726 1931,-732 1931,-732 1931,-744 1931,-744 1931,-750 1925,-756 1919,-756"/>
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 <g id="edge48" class="edge">
 <title>18&#45;&gt;24</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1814.29,-750.8 1823.75,-746.03 1813.38,-743.86 1814.29,-750.8"/>
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 <title>19</title>
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-<text text-anchor="middle" x="1474.5" y="-519.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1516,-540C1516,-540 1433,-540 1433,-540 1427,-540 1421,-534 1421,-528 1421,-528 1421,-516 1421,-516 1421,-510 1427,-504 1433,-504 1433,-504 1516,-504 1516,-504 1522,-504 1528,-510 1528,-516 1528,-516 1528,-528 1528,-528 1528,-534 1522,-540 1516,-540"/>
+<text text-anchor="middle" x="1474.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
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 <!-- 19&#45;&gt;8 -->
 <g id="edge20" class="edge">
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1481.23,-406.28 1478.02,-396.19 1474.24,-406.09 1481.23,-406.28"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1475.0066,-503.7623C1475.6889,-479.201 1476.9098,-435.2474 1477.7124,-406.3541"/>
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 <!-- 20&#45;&gt;9 -->
 <g id="edge21" class="edge">
 <title>20&#45;&gt;9</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1009.54,-333.89 1005.48,-324.1 1002.55,-334.29 1009.54,-333.89"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1007.4906,-359.8314C1007.0628,-352.131 1006.5541,-342.9743 1006.0787,-334.4166"/>
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 <!-- 20&#45;&gt;10 -->
 <g id="edge23" class="edge">
 <title>20&#45;&gt;10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1050.33,-359.88C1073.92,-350.22 1103.56,-338.09 1128.5,-327.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1129.88,-331.1 1137.8,-324.07 1127.22,-324.62 1129.88,-331.1"/>
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 <!-- 20&#45;&gt;11 -->
 <g id="edge25" class="edge">
 <title>20&#45;&gt;11</title>
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 <!-- 20&#45;&gt;12 -->
 <g id="edge27" class="edge">
 <title>20&#45;&gt;12</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="879.2,-324.33 868.61,-324.07 876.72,-330.88 879.2,-324.33"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M961.8167,-359.8314C936.7441,-350.0734 905.6633,-337.977 879.3191,-327.7242"/>
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 <!-- 21&#45;&gt;9 -->
 <g id="edge22" class="edge">
 <title>21&#45;&gt;9</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1053.09,-324.97 1042.54,-324.07 1050.23,-331.36 1053.09,-324.97"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1121.1346,-359.8314C1100.3633,-350.2446 1074.7017,-338.4008 1052.7419,-328.2655"/>
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 <!-- 21&#45;&gt;10 -->
 <g id="edge24" class="edge">
 <title>21&#45;&gt;10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1165.2,-359.7C1167.31,-351.9 1169.86,-342.51 1172.22,-333.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1175.62,-334.67 1174.86,-324.1 1168.86,-332.84 1175.62,-334.67"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1165.2945,-359.8314C1167.3489,-352.0463 1169.796,-342.7729 1172.0756,-334.1347"/>
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 <!-- 21&#45;&gt;11 -->
 <g id="edge26" class="edge">
 <title>21&#45;&gt;11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1210.39,-359.97C1239.15,-350.14 1275.51,-337.73 1305.79,-327.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1307.06,-330.65 1315.39,-324.11 1304.8,-324.03 1307.06,-330.65"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1211.9655,-359.9243C1239.9902,-350.0815 1274.8484,-337.8386 1304.264,-327.5073"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1305.7381,-330.6992 1314.0133,-324.0831 1303.4184,-324.0947 1305.7381,-330.6992"/>
 </g>
 <!-- 21&#45;&gt;12 -->
 <g id="edge28" class="edge">
 <title>21&#45;&gt;12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1097.7,-362.04C1094.59,-361.34 1091.51,-360.66 1088.5,-360 1033.06,-347.91 970.86,-335.42 920.66,-325.6"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="921.27,-322.15 910.79,-323.67 919.93,-329.02 921.27,-322.15"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1097.7102,-362.13C1094.5989,-361.3978 1091.5158,-360.6839 1088.5,-360 1033.0156,-347.4177 970.6855,-334.6484 920.4208,-324.6881"/>
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 </g>
 <!-- 22&#45;&gt;13 -->
 <g id="edge29" class="edge">
 <title>22&#45;&gt;13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1727.75,-719.95C1745.25,-711.98 1762.28,-700.47 1772.5,-684 1780.94,-670.41 1778.95,-662.64 1772.5,-648 1767.51,-636.69 1758.79,-626.74 1749.6,-618.62"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.78,-615.88 1741.84,-612.23 1747.33,-621.28 1751.78,-615.88"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1728.0603,-720.2456C1745.4625,-712.1131 1762.3571,-700.4803 1772.5,-684 1780.8863,-670.3739 1778.8858,-662.6704 1772.5,-648 1767.6585,-636.8773 1759.2717,-627.0106 1750.3561,-618.8541"/>
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 <!-- 23 -->
 <g id="node24" class="node">
 <title>23</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1751.5,-684C1751.5,-684 1579.5,-684 1579.5,-684 1573.5,-684 1567.5,-678 1567.5,-672 1567.5,-672 1567.5,-660 1567.5,-660 1567.5,-654 1573.5,-648 1579.5,-648 1579.5,-648 1751.5,-648 1751.5,-648 1757.5,-648 1763.5,-654 1763.5,-660 1763.5,-660 1763.5,-672 1763.5,-672 1763.5,-678 1757.5,-684 1751.5,-684"/>
-<text text-anchor="middle" x="1665.5" y="-669" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1665.5" y="-658" font-family="sans" font-size="10.00">seqmode: paired_end</text>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1751.5,-684C1751.5,-684 1579.5,-684 1579.5,-684 1573.5,-684 1567.5,-678 1567.5,-672 1567.5,-672 1567.5,-660 1567.5,-660 1567.5,-654 1573.5,-648 1579.5,-648 1579.5,-648 1751.5,-648 1751.5,-648 1757.5,-648 1763.5,-654 1763.5,-660 1763.5,-660 1763.5,-672 1763.5,-672 1763.5,-678 1757.5,-684 1751.5,-684"/>
+<text text-anchor="middle" x="1665.5" y="-669" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1665.5" y="-658" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
 </g>
 <!-- 22&#45;&gt;23 -->
 <g id="edge46" class="edge">
 <title>22&#45;&gt;23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1665.5,-719.7C1665.5,-711.98 1665.5,-702.71 1665.5,-694.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1669,-694.1 1665.5,-684.1 1662,-694.1 1669,-694.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1665.5,-719.8314C1665.5,-712.131 1665.5,-702.9743 1665.5,-694.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1669.0001,-694.4132 1665.5,-684.4133 1662.0001,-694.4133 1669.0001,-694.4132"/>
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 <!-- 31 -->
 <g id="node32" class="node">
 <title>31</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M1517,-612C1517,-612 1422,-612 1422,-612 1416,-612 1410,-606 1410,-600 1410,-600 1410,-588 1410,-588 1410,-582 1416,-576 1422,-576 1422,-576 1517,-576 1517,-576 1523,-576 1529,-582 1529,-588 1529,-588 1529,-600 1529,-600 1529,-606 1523,-612 1517,-612"/>
-<text text-anchor="middle" x="1469.5" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M1517,-612C1517,-612 1422,-612 1422,-612 1416,-612 1410,-606 1410,-600 1410,-600 1410,-588 1410,-588 1410,-582 1416,-576 1422,-576 1422,-576 1517,-576 1517,-576 1523,-576 1529,-582 1529,-588 1529,-588 1529,-600 1529,-600 1529,-606 1523,-612 1517,-612"/>
+<text text-anchor="middle" x="1469.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
 </g>
 <!-- 22&#45;&gt;31 -->
 <g id="edge54" class="edge">
 <title>22&#45;&gt;31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1602.85,-734.4C1527.66,-729.8 1408.21,-717.33 1380.5,-684 1370.27,-671.7 1372.59,-661.91 1380.5,-648 1387.86,-635.04 1399.79,-624.92 1412.55,-617.16"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1414.46,-620.1 1421.47,-612.15 1411.03,-613.99 1414.46,-620.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1602.8337,-735.1678C1527.6304,-730.302 1408.1672,-717.4016 1380.5,-684 1370.2936,-671.6781 1372.6512,-661.9426 1380.5,-648 1387.7034,-635.2038 1399.2994,-625.0907 1411.7742,-617.2465"/>
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 </g>
 <!-- 23&#45;&gt;13 -->
 <g id="edge30" class="edge">
 <title>23&#45;&gt;13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1677.61,-647.7C1683.37,-639.47 1690.36,-629.48 1696.71,-620.42"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1699.66,-622.3 1702.53,-612.1 1693.92,-618.29 1699.66,-622.3"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1677.8648,-647.8314C1683.4509,-639.6232 1690.163,-629.7606 1696.3072,-620.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1699.236,-622.6496 1701.9687,-612.4133 1693.449,-618.7112 1699.236,-622.6496"/>
 </g>
 <!-- 23&#45;&gt;31 -->
 <g id="edge55" class="edge">
 <title>23&#45;&gt;31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1617.8,-647.97C1590.42,-638.19 1555.84,-625.84 1526.97,-615.52"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1528,-612.18 1517.41,-612.11 1525.65,-618.77 1528,-612.18"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1616.2939,-647.9243C1589.6161,-638.1243 1556.4614,-625.945 1528.4148,-615.6422"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1529.3199,-612.246 1518.7263,-612.0831 1526.9062,-618.8167 1529.3199,-612.246"/>
 </g>
 <!-- 24&#45;&gt;14 -->
 <g id="edge31" class="edge">
 <title>24&#45;&gt;14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1931.01,-736.44C1973.04,-732.97 2029.75,-721.05 2062.5,-684 2077.18,-667.39 2079.9,-641.89 2079.4,-622.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2082.89,-622.13 2078.84,-612.34 2075.9,-622.52 2082.89,-622.13"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1931.3273,-728.8736C1979.5156,-719.575 2045.1704,-703.7364 2062.5,-684 2077.1133,-667.3572 2079.9269,-641.985 2079.4782,-622.4174"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2082.9634,-622.0401 2078.9475,-612.2359 2075.9729,-622.4046 2082.9634,-622.0401"/>
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 <!-- 25 -->
 <g id="node26" class="node">
 <title>25</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M2041.5,-684C2041.5,-684 1869.5,-684 1869.5,-684 1863.5,-684 1857.5,-678 1857.5,-672 1857.5,-672 1857.5,-660 1857.5,-660 1857.5,-654 1863.5,-648 1869.5,-648 1869.5,-648 2041.5,-648 2041.5,-648 2047.5,-648 2053.5,-654 2053.5,-660 2053.5,-660 2053.5,-672 2053.5,-672 2053.5,-678 2047.5,-684 2041.5,-684"/>
-<text text-anchor="middle" x="1955.5" y="-669" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1955.5" y="-658" font-family="sans" font-size="10.00">seqmode: single_end</text>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M2041.5,-684C2041.5,-684 1869.5,-684 1869.5,-684 1863.5,-684 1857.5,-678 1857.5,-672 1857.5,-672 1857.5,-660 1857.5,-660 1857.5,-654 1863.5,-648 1869.5,-648 1869.5,-648 2041.5,-648 2041.5,-648 2047.5,-648 2053.5,-654 2053.5,-660 2053.5,-660 2053.5,-672 2053.5,-672 2053.5,-678 2047.5,-684 2041.5,-684"/>
+<text text-anchor="middle" x="1955.5" y="-669" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1955.5" y="-658" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
 </g>
 <!-- 24&#45;&gt;25 -->
 <g id="edge49" class="edge">
 <title>24&#45;&gt;25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1896.78,-719.7C1906.42,-711.05 1918.23,-700.45 1928.73,-691.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1931.34,-693.39 1936.44,-684.1 1926.66,-688.18 1931.34,-693.39"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1897.1827,-719.8314C1906.6051,-711.1337 1918.0401,-700.5783 1928.2796,-691.1265"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1930.8495,-693.5175 1935.8236,-684.1628 1926.1016,-688.3738 1930.8495,-693.5175"/>
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 <g id="node33" class="node">
 <title>32</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M1654,-612C1654,-612 1559,-612 1559,-612 1553,-612 1547,-606 1547,-600 1547,-600 1547,-588 1547,-588 1547,-582 1553,-576 1559,-576 1559,-576 1654,-576 1654,-576 1660,-576 1666,-582 1666,-588 1666,-588 1666,-600 1666,-600 1666,-606 1660,-612 1654,-612"/>
-<text text-anchor="middle" x="1606.5" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M1654,-612C1654,-612 1559,-612 1559,-612 1553,-612 1547,-606 1547,-600 1547,-600 1547,-588 1547,-588 1547,-582 1553,-576 1559,-576 1559,-576 1654,-576 1654,-576 1660,-576 1666,-582 1666,-588 1666,-588 1666,-600 1666,-600 1666,-606 1660,-612 1654,-612"/>
+<text text-anchor="middle" x="1606.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
 </g>
 <!-- 24&#45;&gt;32 -->
 <g id="edge57" class="edge">
 <title>24&#45;&gt;32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1861.6,-719.93C1842.27,-700.09 1807.82,-667.58 1772.5,-648 1755.44,-638.54 1713.43,-625.16 1675.95,-614.21"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1676.61,-610.76 1666.03,-611.34 1674.66,-617.48 1676.61,-610.76"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1860.5781,-719.6848C1841.0852,-699.561 1807.253,-667.5109 1772.5,-648 1755.4585,-638.4326 1713.4539,-624.7991 1675.9648,-613.625"/>
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 <g id="edge32" class="edge">
 <title>25&#45;&gt;14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1985.1,-647.88C2001.07,-638.64 2020.96,-627.13 2038.11,-617.21"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2039.88,-620.23 2046.79,-612.19 2036.38,-614.17 2039.88,-620.23"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1986.0334,-647.8314C2001.6282,-638.5518 2020.7768,-627.1576 2037.4354,-617.2451"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2039.5916,-620.0348 2046.3955,-611.9134 2036.0121,-614.0193 2039.5916,-620.0348"/>
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 <!-- 25&#45;&gt;32 -->
 <g id="edge58" class="edge">
 <title>25&#45;&gt;32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1858.37,-647.96C1806.91,-638.61 1742.42,-626.39 1676.09,-612.07"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1676.81,-608.64 1666.29,-609.94 1675.32,-615.49 1676.81,-608.64"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1857.3424,-648.6759C1806.1098,-639.2504 1742.2062,-626.8981 1676.4252,-612.1395"/>
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 <g id="node27" class="node">
 <title>26</title>
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-<text text-anchor="middle" x="1982.5" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M2028.5,-396C2028.5,-396 1936.5,-396 1936.5,-396 1930.5,-396 1924.5,-390 1924.5,-384 1924.5,-384 1924.5,-372 1924.5,-372 1924.5,-366 1930.5,-360 1936.5,-360 1936.5,-360 2028.5,-360 2028.5,-360 2034.5,-360 2040.5,-366 2040.5,-372 2040.5,-372 2040.5,-384 2040.5,-384 2040.5,-390 2034.5,-396 2028.5,-396"/>
+<text text-anchor="middle" x="1982.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
 </g>
 <!-- 26&#45;&gt;15 -->
 <g id="edge33" class="edge">
 <title>26&#45;&gt;15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1949.72,-359.88C1931.87,-350.55 1909.6,-338.92 1890.5,-328.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1891.89,-325.72 1881.41,-324.19 1888.65,-331.92 1891.89,-325.72"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1948.6861,-359.8314C1931.2293,-350.4516 1909.7513,-338.9112 1891.1648,-328.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1892.7686,-325.8129 1882.303,-324.1628 1889.4554,-331.9792 1892.7686,-325.8129"/>
 </g>
 <!-- 27 -->
 <g id="node28" class="node">
 <title>27</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1894.5,-396C1894.5,-396 1802.5,-396 1802.5,-396 1796.5,-396 1790.5,-390 1790.5,-384 1790.5,-384 1790.5,-372 1790.5,-372 1790.5,-366 1796.5,-360 1802.5,-360 1802.5,-360 1894.5,-360 1894.5,-360 1900.5,-360 1906.5,-366 1906.5,-372 1906.5,-372 1906.5,-384 1906.5,-384 1906.5,-390 1900.5,-396 1894.5,-396"/>
-<text text-anchor="middle" x="1848.5" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1894.5,-396C1894.5,-396 1802.5,-396 1802.5,-396 1796.5,-396 1790.5,-390 1790.5,-384 1790.5,-384 1790.5,-372 1790.5,-372 1790.5,-366 1796.5,-360 1802.5,-360 1802.5,-360 1894.5,-360 1894.5,-360 1900.5,-360 1906.5,-366 1906.5,-372 1906.5,-372 1906.5,-384 1906.5,-384 1906.5,-390 1900.5,-396 1894.5,-396"/>
+<text text-anchor="middle" x="1848.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
 </g>
 <!-- 27&#45;&gt;15 -->
 <g id="edge34" class="edge">
 <title>27&#45;&gt;15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1848.5,-359.7C1848.5,-351.98 1848.5,-342.71 1848.5,-334.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1852,-334.1 1848.5,-324.1 1845,-334.1 1852,-334.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1848.5,-359.8314C1848.5,-352.131 1848.5,-342.9743 1848.5,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1852.0001,-334.4132 1848.5,-324.4133 1845.0001,-334.4133 1852.0001,-334.4132"/>
 </g>
 <!-- 28 -->
 <g id="node29" class="node">
 <title>28</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1119,-905C1119,-905 818,-905 818,-905 812,-905 806,-899 806,-893 806,-893 806,-881 806,-881 806,-875 812,-869 818,-869 818,-869 1119,-869 1119,-869 1125,-869 1131,-875 1131,-881 1131,-881 1131,-893 1131,-893 1131,-899 1125,-905 1119,-905"/>
-<text text-anchor="middle" x="968.5" y="-890" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="968.5" y="-879" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1119,-905C1119,-905 818,-905 818,-905 812,-905 806,-899 806,-893 806,-893 806,-881 806,-881 806,-875 812,-869 818,-869 818,-869 1119,-869 1119,-869 1125,-869 1131,-875 1131,-881 1131,-881 1131,-893 1131,-893 1131,-899 1125,-905 1119,-905"/>
+<text text-anchor="middle" x="968.5" y="-890" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="968.5" y="-879" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
 </g>
 <!-- 28&#45;&gt;16 -->
 <g id="edge35" class="edge">
 <title>28&#45;&gt;16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M968.5,-868.82C968.5,-860.42 968.5,-850.12 968.5,-840.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="972,-840.56 968.5,-830.56 965,-840.56 972,-840.56"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M968.5,-868.9656C968.5,-860.5178 968.5,-850.2542 968.5,-840.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="972.0001,-840.6265 968.5,-830.6265 965.0001,-840.6265 972.0001,-840.6265"/>
 </g>
 <!-- 29 -->
 <g id="node30" class="node">
 <title>29</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M1185,-540C1185,-540 1070,-540 1070,-540 1064,-540 1058,-534 1058,-528 1058,-528 1058,-516 1058,-516 1058,-510 1064,-504 1070,-504 1070,-504 1185,-504 1185,-504 1191,-504 1197,-510 1197,-516 1197,-516 1197,-528 1197,-528 1197,-534 1191,-540 1185,-540"/>
-<text text-anchor="middle" x="1127.5" y="-525" font-family="sans" font-size="10.00">extract_transcriptome</text>
-<text text-anchor="middle" x="1127.5" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1185,-540C1185,-540 1070,-540 1070,-540 1064,-540 1058,-534 1058,-528 1058,-528 1058,-516 1058,-516 1058,-510 1064,-504 1070,-504 1070,-504 1185,-504 1185,-504 1191,-504 1197,-510 1197,-516 1197,-516 1197,-528 1197,-528 1197,-534 1191,-540 1185,-540"/>
+<text text-anchor="middle" x="1127.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<text text-anchor="middle" x="1127.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
 </g>
 <!-- 29&#45;&gt;17 -->
 <g id="edge36" class="edge">
 <title>29&#45;&gt;17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1144.56,-503.7C1153,-495.14 1163.32,-484.66 1172.54,-475.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1175.11,-477.68 1179.64,-468.1 1170.13,-472.77 1175.11,-477.68"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1144.9116,-503.8314C1153.021,-495.3694 1162.8156,-485.1489 1171.682,-475.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1174.4618,-478.0549 1178.854,-468.4133 1169.4079,-473.2115 1174.4618,-478.0549"/>
 </g>
 <!-- 33 -->
 <g id="node34" class="node">
 <title>33</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1106,-468C1106,-468 1009,-468 1009,-468 1003,-468 997,-462 997,-456 997,-456 997,-444 997,-444 997,-438 1003,-432 1009,-432 1009,-432 1106,-432 1106,-432 1112,-432 1118,-438 1118,-444 1118,-444 1118,-456 1118,-456 1118,-462 1112,-468 1106,-468"/>
-<text text-anchor="middle" x="1057.5" y="-453" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="1057.5" y="-442" font-family="sans" font-size="10.00">kmer: 31</text>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1106,-468C1106,-468 1009,-468 1009,-468 1003,-468 997,-462 997,-456 997,-456 997,-444 997,-444 997,-438 1003,-432 1009,-432 1009,-432 1106,-432 1106,-432 1112,-432 1118,-438 1118,-444 1118,-444 1118,-456 1118,-456 1118,-462 1112,-468 1106,-468"/>
+<text text-anchor="middle" x="1057.5" y="-453" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<text text-anchor="middle" x="1057.5" y="-442" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
 </g>
 <!-- 29&#45;&gt;33 -->
 <g id="edge60" class="edge">
 <title>29&#45;&gt;33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1110.2,-503.7C1101.64,-495.14 1091.16,-484.66 1081.8,-475.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1084.15,-472.7 1074.6,-468.1 1079.2,-477.65 1084.15,-472.7"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1109.836,-503.8314C1101.5268,-495.2848 1091.4736,-484.9443 1082.4082,-475.6198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1084.8821,-473.1435 1075.4018,-468.4133 1079.8631,-478.023 1084.8821,-473.1435"/>
 </g>
 <!-- 30 -->
 <g id="node31" class="node">
 <title>30</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M1480,-905C1480,-905 1167,-905 1167,-905 1161,-905 1155,-899 1155,-893 1155,-893 1155,-881 1155,-881 1155,-875 1161,-869 1167,-869 1167,-869 1480,-869 1480,-869 1486,-869 1492,-875 1492,-881 1492,-881 1492,-893 1492,-893 1492,-899 1486,-905 1480,-905"/>
-<text text-anchor="middle" x="1323.5" y="-890" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1323.5" y="-879" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M1480,-905C1480,-905 1167,-905 1167,-905 1161,-905 1155,-899 1155,-893 1155,-893 1155,-881 1155,-881 1155,-875 1161,-869 1167,-869 1167,-869 1480,-869 1480,-869 1486,-869 1492,-875 1492,-881 1492,-881 1492,-893 1492,-893 1492,-899 1486,-905 1480,-905"/>
+<text text-anchor="middle" x="1323.5" y="-890" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1323.5" y="-879" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
 </g>
 <!-- 30&#45;&gt;18 -->
 <g id="edge37" class="edge">
 <title>30&#45;&gt;18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1323.5,-868.82C1323.5,-860.42 1323.5,-850.12 1323.5,-840.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1327,-840.56 1323.5,-830.56 1320,-840.56 1327,-840.56"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1323.5,-868.9656C1323.5,-860.5178 1323.5,-850.2542 1323.5,-840.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1327.0001,-840.6265 1323.5,-830.6265 1320.0001,-840.6265 1327.0001,-840.6265"/>
 </g>
 <!-- 31&#45;&gt;19 -->
 <g id="edge38" class="edge">
 <title>31&#45;&gt;19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1470.74,-575.7C1471.29,-567.98 1471.95,-558.71 1472.56,-550.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1476.06,-550.33 1473.28,-540.1 1469.07,-549.83 1476.06,-550.33"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1470.7617,-575.8314C1471.2965,-568.131 1471.9323,-558.9743 1472.5266,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1476.02,-550.6317 1473.2213,-540.4133 1469.0368,-550.1467 1476.02,-550.6317"/>
 </g>
 <!-- 32&#45;&gt;19 -->
 <g id="edge39" class="edge">
 <title>32&#45;&gt;19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1574.21,-575.88C1556.63,-566.55 1534.69,-554.92 1515.87,-544.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1517.39,-541.78 1506.91,-540.19 1514.11,-547.97 1517.39,-541.78"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1573.1908,-575.8314C1556.0727,-566.4942 1535.0294,-555.016 1516.7778,-545.0606"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1518.2535,-541.8788 1507.7985,-540.1628 1514.9015,-548.024 1518.2535,-541.8788"/>
 </g>
 <!-- 33&#45;&gt;20 -->
 <g id="edge41" class="edge">
 <title>33&#45;&gt;20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1045.39,-431.7C1039.63,-423.47 1032.64,-413.48 1026.29,-404.42"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1029.08,-402.29 1020.47,-396.1 1023.34,-406.3 1029.08,-402.29"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1045.1352,-431.8314C1039.5491,-423.6232 1032.837,-413.7606 1026.6928,-404.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1029.551,-402.7112 1021.0313,-396.4133 1023.764,-406.6496 1029.551,-402.7112"/>
 </g>
 <!-- 33&#45;&gt;21 -->
 <g id="edge43" class="edge">
 <title>33&#45;&gt;21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1082.7,-431.88C1095.91,-422.89 1112.29,-411.76 1126.61,-402.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1128.9,-404.71 1135.21,-396.19 1124.97,-398.92 1128.9,-404.71"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1083.4912,-431.8314C1096.4216,-422.7927 1112.2222,-411.7476 1126.1383,-402.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1128.3263,-404.7608 1134.5171,-396.1628 1124.3157,-399.0235 1128.3263,-404.7608"/>
 </g>
 <!-- 34 -->
 <g id="node35" class="node">
 <title>34</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M1935,-833C1935,-833 1820,-833 1820,-833 1814,-833 1808,-827 1808,-821 1808,-821 1808,-804 1808,-804 1808,-798 1814,-792 1820,-792 1820,-792 1935,-792 1935,-792 1941,-792 1947,-798 1947,-804 1947,-804 1947,-821 1947,-821 1947,-827 1941,-833 1935,-833"/>
-<text text-anchor="middle" x="1877.5" y="-821" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="1877.5" y="-810" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1877.5" y="-799" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M1935,-833C1935,-833 1820,-833 1820,-833 1814,-833 1808,-827 1808,-821 1808,-821 1808,-804 1808,-804 1808,-798 1814,-792 1820,-792 1820,-792 1935,-792 1935,-792 1941,-792 1947,-798 1947,-804 1947,-804 1947,-821 1947,-821 1947,-827 1941,-833 1935,-833"/>
+<text text-anchor="middle" x="1877.5" y="-821" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<text text-anchor="middle" x="1877.5" y="-810" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
+<text text-anchor="middle" x="1877.5" y="-799" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
 </g>
 <!-- 34&#45;&gt;22 -->
 <g id="edge44" class="edge">
 <title>34&#45;&gt;22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1820.41,-791.98C1790.86,-781.87 1754.82,-769.55 1724.94,-759.33"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1726.07,-756.01 1715.47,-756.09 1723.8,-762.64 1726.07,-756.01"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1819.0089,-791.9453C1790.2695,-781.8459 1755.6554,-769.682 1726.576,-759.463"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1727.5378,-756.0912 1716.9429,-756.0778 1725.2169,-762.6953 1727.5378,-756.0912"/>
 </g>
 <!-- 34&#45;&gt;24 -->
 <g id="edge47" class="edge">
 <title>34&#45;&gt;24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1877.5,-791.69C1877.5,-783.91 1877.5,-774.84 1877.5,-766.45"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1881,-766.32 1877.5,-756.32 1874,-766.32 1881,-766.32"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1877.5,-791.7476C1877.5,-783.8767 1877.5,-774.7743 1877.5,-766.3232"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1881.0001,-766.1086 1877.5,-756.1087 1874.0001,-766.1087 1881.0001,-766.1086"/>
 </g>
 <!-- 41 -->
 <g id="node42" class="node">
 <title>41</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M2180.5,-540C2180.5,-540 2088.5,-540 2088.5,-540 2082.5,-540 2076.5,-534 2076.5,-528 2076.5,-528 2076.5,-516 2076.5,-516 2076.5,-510 2082.5,-504 2088.5,-504 2088.5,-504 2180.5,-504 2180.5,-504 2186.5,-504 2192.5,-510 2192.5,-516 2192.5,-516 2192.5,-528 2192.5,-528 2192.5,-534 2186.5,-540 2180.5,-540"/>
-<text text-anchor="middle" x="2134.5" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M2180.5,-540C2180.5,-540 2088.5,-540 2088.5,-540 2082.5,-540 2076.5,-534 2076.5,-528 2076.5,-528 2076.5,-516 2076.5,-516 2076.5,-510 2082.5,-504 2088.5,-504 2088.5,-504 2180.5,-504 2180.5,-504 2186.5,-504 2192.5,-510 2192.5,-516 2192.5,-516 2192.5,-528 2192.5,-528 2192.5,-534 2186.5,-540 2180.5,-540"/>
+<text text-anchor="middle" x="2134.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
 </g>
 <!-- 34&#45;&gt;41 -->
 <g id="edge70" class="edge">
 <title>34&#45;&gt;41</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1925.31,-791.96C1971.15,-771.14 2039.67,-734.23 2083.5,-684 2116.9,-645.72 2128.45,-585.52 2132.43,-550.59"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2135.95,-550.5 2133.47,-540.2 2128.99,-549.8 2135.95,-550.5"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1927.0531,-791.9156C1972.8687,-770.722 2040.2186,-733.7833 2083.5,-684 2116.8987,-645.584 2128.4448,-585.3066 2132.4228,-550.1245"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2135.9164,-550.3626 2133.4302,-540.0636 2128.9512,-549.6651 2135.9164,-550.3626"/>
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 <!-- 35 -->
 <g id="node36" class="node">
 <title>35</title>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 0ee15456fdf3eba98f041b3e5d56ea0ec22cb18c..d5f3ea24e68aae2d8df330f9bd363551def62199 100644
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-<text text-anchor="middle" x="338.5" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M392.5,-180C392.5,-180 284.5,-180 284.5,-180 278.5,-180 272.5,-174 272.5,-168 272.5,-168 272.5,-156 272.5,-156 272.5,-150 278.5,-144 284.5,-144 284.5,-144 392.5,-144 392.5,-144 398.5,-144 404.5,-150 404.5,-156 404.5,-156 404.5,-168 404.5,-168 404.5,-174 398.5,-180 392.5,-180"/>
+<text text-anchor="middle" x="338.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_MultiQC_config</text>
 </g>
 <!-- 2&#45;&gt;1 -->
 <g id="edge2" class="edge">
 <title>2&#45;&gt;1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M338.5,-143.7C338.5,-135.98 338.5,-126.71 338.5,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="342,-118.1 338.5,-108.1 335,-118.1 342,-118.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M338.5,-143.8314C338.5,-136.131 338.5,-126.9743 338.5,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="342.0001,-118.4132 338.5,-108.4133 335.0001,-118.4133 342.0001,-118.4132"/>
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 <!-- 3 -->
 <g id="node4" class="node">
 <title>3</title>
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-<text text-anchor="middle" x="338.5" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M393,-252C393,-252 284,-252 284,-252 278,-252 272,-246 272,-240 272,-240 272,-228 272,-228 272,-222 278,-216 284,-216 284,-216 393,-216 393,-216 399,-216 405,-222 405,-228 405,-228 405,-240 405,-240 405,-246 399,-252 393,-252"/>
+<text text-anchor="middle" x="338.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_files_for_report</text>
 </g>
 <!-- 3&#45;&gt;2 -->
 <g id="edge3" class="edge">
 <title>3&#45;&gt;2</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M338.5,-215.7C338.5,-207.98 338.5,-198.71 338.5,-190.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="342,-190.1 338.5,-180.1 335,-190.1 342,-190.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M338.5,-215.8314C338.5,-208.131 338.5,-198.9743 338.5,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="342.0001,-190.4132 338.5,-180.4133 335.0001,-190.4133 342.0001,-190.4132"/>
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 <!-- 4 -->
 <g id="node5" class="node">
 <title>4</title>
 <path fill="none" stroke="#56d0d8" stroke-width="2" d="M84.5,-324C84.5,-324 44.5,-324 44.5,-324 38.5,-324 32.5,-318 32.5,-312 32.5,-312 32.5,-300 32.5,-300 32.5,-294 38.5,-288 44.5,-288 44.5,-288 84.5,-288 84.5,-288 90.5,-288 96.5,-294 96.5,-300 96.5,-300 96.5,-312 96.5,-312 96.5,-318 90.5,-324 84.5,-324"/>
-<text text-anchor="middle" x="64.5" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="64.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
 </g>
 <!-- 4&#45;&gt;3 -->
-<g id="edge10" class="edge">
+<g id="edge8" class="edge">
 <title>4&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M96.54,-291.11C99.54,-289.99 102.56,-288.94 105.5,-288 156.87,-271.64 216.14,-258.23 262.04,-248.99"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="262.79,-252.41 271.92,-247.03 261.43,-245.54 262.79,-252.41"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M96.5074,-291.2746C99.5193,-290.0936 102.549,-288.9803 105.5,-288 156.7139,-270.9876 215.9793,-257.3312 261.9218,-248.0079"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="262.694,-251.4228 271.8113,-246.026 261.3185,-244.5593 262.694,-251.4228"/>
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 <!-- 5 -->
 <g id="node6" class="node">
 <title>5</title>
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-<text text-anchor="middle" x="141.5" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M156.5,-324C156.5,-324 126.5,-324 126.5,-324 120.5,-324 114.5,-318 114.5,-312 114.5,-312 114.5,-300 114.5,-300 114.5,-294 120.5,-288 126.5,-288 126.5,-288 156.5,-288 156.5,-288 162.5,-288 168.5,-294 168.5,-300 168.5,-300 168.5,-312 168.5,-312 168.5,-318 162.5,-324 156.5,-324"/>
+<text text-anchor="middle" x="141.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
 </g>
 <!-- 5&#45;&gt;3 -->
-<g id="edge7" class="edge">
+<g id="edge4" class="edge">
 <title>5&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M168.75,-293.41C173.32,-291.55 178.03,-289.68 182.5,-288 212.91,-276.54 247.05,-264.82 275.62,-255.32"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="277.09,-258.52 285.48,-252.05 274.89,-251.87 277.09,-258.52"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M168.719,-293.6855C173.2937,-291.721 178.0125,-289.7585 182.5,-288 211.9795,-276.4482 245.0674,-264.8103 273.1593,-255.3118"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="274.5106,-258.5501 282.8733,-252.045 272.2793,-251.9152 274.5106,-258.5501"/>
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 <!-- 6 -->
 <g id="node7" class="node">
 <title>6</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M175,-756C175,-756 12,-756 12,-756 6,-756 0,-750 0,-744 0,-744 0,-732 0,-732 0,-726 6,-720 12,-720 12,-720 175,-720 175,-720 181,-720 187,-726 187,-732 187,-732 187,-744 187,-744 187,-750 181,-756 175,-756"/>
-<text text-anchor="middle" x="93.5" y="-735.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M175,-756C175,-756 12,-756 12,-756 6,-756 0,-750 0,-744 0,-744 0,-732 0,-732 0,-726 6,-720 12,-720 12,-720 175,-720 175,-720 181,-720 187,-726 187,-732 187,-732 187,-744 187,-744 187,-750 181,-756 175,-756"/>
+<text text-anchor="middle" x="93.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
 </g>
 <!-- 6&#45;&gt;3 -->
-<g id="edge5" class="edge">
+<g id="edge7" class="edge">
 <title>6&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M117.13,-719.97C147.54,-695.89 196.5,-648.75 196.5,-595 196.5,-595 196.5,-595 196.5,-377 196.5,-331.63 214.59,-320.25 246.5,-288 258.74,-275.63 274.46,-265.17 289.44,-256.91"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="291.42,-259.81 298.62,-252.04 288.15,-253.63 291.42,-259.81"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M118.1711,-719.8169C148.6427,-695.0584 196.5,-647.6361 196.5,-594 196.5,-594 196.5,-594 196.5,-378 196.5,-322.7192 250.2129,-280.9675 291.5688,-257.0138"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="293.4399,-259.9773 300.4466,-252.0302 290.0133,-253.8733 293.4399,-259.9773"/>
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 <!-- 7 -->
 <g id="node8" class="node">
 <title>7</title>
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-<text text-anchor="middle" x="290.5" y="-735.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M363.5,-756C363.5,-756 217.5,-756 217.5,-756 211.5,-756 205.5,-750 205.5,-744 205.5,-744 205.5,-732 205.5,-732 205.5,-726 211.5,-720 217.5,-720 217.5,-720 363.5,-720 363.5,-720 369.5,-720 375.5,-726 375.5,-732 375.5,-732 375.5,-744 375.5,-744 375.5,-750 369.5,-756 363.5,-756"/>
+<text text-anchor="middle" x="290.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
 </g>
 <!-- 7&#45;&gt;3 -->
-<g id="edge11" class="edge">
+<g id="edge5" class="edge">
 <title>7&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="308.8,-261.19 314.38,-252.18 304.4,-255.74 308.8,-261.19"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M275.1841,-719.5801C267.614,-709.608 258.9551,-696.7465 253.5,-684 237.415,-646.4157 234.5,-634.8816 234.5,-594 234.5,-594 234.5,-594 234.5,-378 234.5,-328.6014 275.2193,-284.6421 305.6997,-258.6562"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="308.1152,-261.2004 313.5894,-252.1293 303.6533,-255.8068 308.1152,-261.2004"/>
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 <!-- 8 -->
 <g id="node9" class="node">
 <title>8</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M582.5,-396C582.5,-396 512.5,-396 512.5,-396 506.5,-396 500.5,-390 500.5,-384 500.5,-384 500.5,-372 500.5,-372 500.5,-366 506.5,-360 512.5,-360 512.5,-360 582.5,-360 582.5,-360 588.5,-360 594.5,-366 594.5,-372 594.5,-372 594.5,-384 594.5,-384 594.5,-390 588.5,-396 582.5,-396"/>
-<text text-anchor="middle" x="547.5" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M582.5,-396C582.5,-396 512.5,-396 512.5,-396 506.5,-396 500.5,-390 500.5,-384 500.5,-384 500.5,-372 500.5,-372 500.5,-366 506.5,-360 512.5,-360 512.5,-360 582.5,-360 582.5,-360 588.5,-360 594.5,-366 594.5,-372 594.5,-372 594.5,-384 594.5,-384 594.5,-390 588.5,-396 582.5,-396"/>
+<text text-anchor="middle" x="547.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
 </g>
 <!-- 8&#45;&gt;3 -->
-<g id="edge12" class="edge">
+<g id="edge10" class="edge">
 <title>8&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M534.73,-359.93C519.39,-340.39 492,-308.45 462.5,-288 443.65,-274.93 421.06,-264.1 400.35,-255.71"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="401.58,-252.43 391,-252.03 399.02,-258.95 401.58,-252.43"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M533.9147,-359.6949C518.4412,-339.8788 491.5187,-308.3829 462.5,-288 444.171,-275.1256 422.2843,-264.348 402.0362,-255.8921"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="403.1424,-252.5639 392.56,-252.0501 400.5123,-259.051 403.1424,-252.5639"/>
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 <!-- 9 -->
 <g id="node10" class="node">
 <title>9</title>
 <path fill="none" stroke="#56d8b9" stroke-width="2" d="M402.5,-684C402.5,-684 274.5,-684 274.5,-684 268.5,-684 262.5,-678 262.5,-672 262.5,-672 262.5,-660 262.5,-660 262.5,-654 268.5,-648 274.5,-648 274.5,-648 402.5,-648 402.5,-648 408.5,-648 414.5,-654 414.5,-660 414.5,-660 414.5,-672 414.5,-672 414.5,-678 408.5,-684 402.5,-684"/>
-<text text-anchor="middle" x="338.5" y="-663.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="338.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
 </g>
 <!-- 9&#45;&gt;3 -->
-<g id="edge9" class="edge">
+<g id="edge6" class="edge">
 <title>9&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="342,-262.05 338.5,-252.05 335,-262.05 342,-262.05"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M338.5,-647.8146C338.5,-620.4983 338.5,-567.25 338.5,-522 338.5,-522 338.5,-522 338.5,-378 338.5,-337.876 338.5,-291.4631 338.5,-262.4177"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="342.0001,-262.1853 338.5,-252.1854 335.0001,-262.1854 342.0001,-262.1853"/>
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 <!-- 10 -->
 <g id="node11" class="node">
 <title>10</title>
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-<text text-anchor="middle" x="519.5" y="-663.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M594.5,-684C594.5,-684 444.5,-684 444.5,-684 438.5,-684 432.5,-678 432.5,-672 432.5,-672 432.5,-660 432.5,-660 432.5,-654 438.5,-648 444.5,-648 444.5,-648 594.5,-648 594.5,-648 600.5,-648 606.5,-654 606.5,-660 606.5,-660 606.5,-672 606.5,-672 606.5,-678 600.5,-684 594.5,-684"/>
+<text text-anchor="middle" x="519.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
 </g>
 <!-- 10&#45;&gt;3 -->
-<g id="edge6" class="edge">
+<g id="edge11" class="edge">
 <title>10&#45;&gt;3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="374.38,-255.29 364.29,-252.06 370.16,-260.88 374.38,-255.29"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M503.7428,-647.8597C482.8256,-621.8524 448.5,-571.6151 448.5,-522 448.5,-522 448.5,-522 448.5,-378 448.5,-327.5369 405.3128,-283.7768 373.0594,-258.1321"/>
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 <g id="node12" class="node">
 <title>11</title>
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-<text text-anchor="middle" x="971.5" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M989.5,-612C989.5,-612 953.5,-612 953.5,-612 947.5,-612 941.5,-606 941.5,-600 941.5,-600 941.5,-588 941.5,-588 941.5,-582 947.5,-576 953.5,-576 953.5,-576 989.5,-576 989.5,-576 995.5,-576 1001.5,-582 1001.5,-588 1001.5,-588 1001.5,-600 1001.5,-600 1001.5,-606 995.5,-612 989.5,-612"/>
+<text text-anchor="middle" x="971.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
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-<g id="edge8" class="edge">
+<g id="edge12" class="edge">
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="415.41,-231.54 405.28,-234.64 415.13,-238.54 415.41,-231.54"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M941.3162,-586.1618C866.1306,-565.7547 676.5,-508.4873 676.5,-450 676.5,-450 676.5,-450 676.5,-378 676.5,-321.5184 514.7343,-274.2676 415.0242,-250.5076"/>
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 <g id="node32" class="node">
 <title>31</title>
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-<text text-anchor="middle" x="971.5" y="-519.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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+<text text-anchor="middle" x="971.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
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 <g id="edge48" class="edge">
 <title>11&#45;&gt;31</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="975,-550.1 971.5,-540.1 968,-550.1 975,-550.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M971.5,-575.8314C971.5,-568.131 971.5,-558.9743 971.5,-550.4166"/>
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 <g id="node13" class="node">
 <title>12</title>
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-<text text-anchor="middle" x="845.5" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M889,-324C889,-324 802,-324 802,-324 796,-324 790,-318 790,-312 790,-312 790,-300 790,-300 790,-294 796,-288 802,-288 802,-288 889,-288 889,-288 895,-288 901,-294 901,-300 901,-300 901,-312 901,-312 901,-318 895,-324 889,-324"/>
+<text text-anchor="middle" x="845.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
 </g>
 <!-- 12&#45;&gt;3 -->
-<g id="edge4" class="edge">
+<g id="edge9" class="edge">
 <title>12&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M789.79,-297.31C698.8,-284.75 518.14,-259.8 415.13,-245.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="415.49,-242.1 405.11,-244.2 414.53,-249.03 415.49,-242.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M789.7918,-298.0888C698.802,-285.1672 518.1379,-259.5107 415.1331,-244.8828"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="415.5004,-241.3999 405.1076,-243.4591 414.5161,-248.3304 415.5004,-241.3999"/>
 </g>
 <!-- 13 -->
 <g id="node14" class="node">
 <title>13</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M446.5,-828C446.5,-828 318.5,-828 318.5,-828 312.5,-828 306.5,-822 306.5,-816 306.5,-816 306.5,-804 306.5,-804 306.5,-798 312.5,-792 318.5,-792 318.5,-792 446.5,-792 446.5,-792 452.5,-792 458.5,-798 458.5,-804 458.5,-804 458.5,-816 458.5,-816 458.5,-822 452.5,-828 446.5,-828"/>
-<text text-anchor="middle" x="382.5" y="-807.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M446.5,-828C446.5,-828 318.5,-828 318.5,-828 312.5,-828 306.5,-822 306.5,-816 306.5,-816 306.5,-804 306.5,-804 306.5,-798 312.5,-792 318.5,-792 318.5,-792 446.5,-792 446.5,-792 452.5,-792 458.5,-798 458.5,-804 458.5,-804 458.5,-816 458.5,-816 458.5,-822 452.5,-828 446.5,-828"/>
+<text text-anchor="middle" x="382.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
 </g>
 <!-- 13&#45;&gt;6 -->
-<g id="edge14" class="edge">
+<g id="edge13" class="edge">
 <title>13&#45;&gt;6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M312.17,-791.97C270.4,-781.85 217.28,-768.98 173.85,-758.46"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="174.44,-755 163.89,-756.05 172.79,-761.81 174.44,-755"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M309.9461,-791.9243C269.0723,-781.7412 217.8873,-768.9892 175.5552,-758.4428"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="176.3826,-755.042 165.833,-756.0207 174.6903,-761.8344 176.3826,-755.042"/>
 </g>
 <!-- 17 -->
 <g id="node18" class="node">
 <title>17</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M523.5,-756C523.5,-756 405.5,-756 405.5,-756 399.5,-756 393.5,-750 393.5,-744 393.5,-744 393.5,-732 393.5,-732 393.5,-726 399.5,-720 405.5,-720 405.5,-720 523.5,-720 523.5,-720 529.5,-720 535.5,-726 535.5,-732 535.5,-732 535.5,-744 535.5,-744 535.5,-750 529.5,-756 523.5,-756"/>
-<text text-anchor="middle" x="464.5" y="-735.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M523.5,-756C523.5,-756 405.5,-756 405.5,-756 399.5,-756 393.5,-750 393.5,-744 393.5,-744 393.5,-732 393.5,-732 393.5,-726 399.5,-720 405.5,-720 405.5,-720 523.5,-720 523.5,-720 529.5,-720 535.5,-726 535.5,-732 535.5,-732 535.5,-744 535.5,-744 535.5,-750 529.5,-756 523.5,-756"/>
+<text text-anchor="middle" x="464.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
 </g>
 <!-- 13&#45;&gt;17 -->
-<g id="edge31" class="edge">
+<g id="edge30" class="edge">
 <title>13&#45;&gt;17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M402.77,-791.7C413,-782.97 425.56,-772.24 436.68,-762.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="439.13,-765.26 444.46,-756.1 434.59,-759.94 439.13,-765.26"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M403.1921,-791.8314C413.1948,-783.0485 425.355,-772.3712 436.1999,-762.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="438.6094,-765.3909 443.8146,-756.1628 433.9908,-760.1308 438.6094,-765.3909"/>
 </g>
 <!-- 19 -->
 <g id="node20" class="node">
 <title>19</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M981,-756C981,-756 880,-756 880,-756 874,-756 868,-750 868,-744 868,-744 868,-732 868,-732 868,-726 874,-720 880,-720 880,-720 981,-720 981,-720 987,-720 993,-726 993,-732 993,-732 993,-744 993,-744 993,-750 987,-756 981,-756"/>
-<text text-anchor="middle" x="930.5" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M981,-756C981,-756 880,-756 880,-756 874,-756 868,-750 868,-744 868,-744 868,-732 868,-732 868,-726 874,-720 880,-720 880,-720 981,-720 981,-720 987,-720 993,-726 993,-732 993,-732 993,-744 993,-744 993,-750 987,-756 981,-756"/>
+<text text-anchor="middle" x="930.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
 </g>
 <!-- 13&#45;&gt;19 -->
 <g id="edge35" class="edge">
 <title>13&#45;&gt;19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M458.9,-793.41C461.8,-792.91 464.68,-792.44 467.5,-792 604.82,-770.45 766.37,-753.95 857.77,-745.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="858.11,-748.92 867.74,-744.51 857.46,-741.95 858.11,-748.92"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M458.8927,-793.4742C461.795,-792.9571 464.6717,-792.4634 467.5,-792 604.7105,-769.5199 766.2912,-752.8915 857.7293,-744.3857"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="858.0763,-747.8686 867.7119,-743.4635 857.4323,-740.8983 858.0763,-747.8686"/>
 </g>
 <!-- 14 -->
 <g id="node15" class="node">
 <title>14</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M272,-828C272,-828 175,-828 175,-828 169,-828 163,-822 163,-816 163,-816 163,-804 163,-804 163,-798 169,-792 175,-792 175,-792 272,-792 272,-792 278,-792 284,-798 284,-804 284,-804 284,-816 284,-816 284,-822 278,-828 272,-828"/>
-<text text-anchor="middle" x="223.5" y="-807.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M272,-828C272,-828 175,-828 175,-828 169,-828 163,-822 163,-816 163,-816 163,-804 163,-804 163,-798 169,-792 175,-792 175,-792 272,-792 272,-792 278,-792 284,-798 284,-804 284,-804 284,-816 284,-816 284,-822 278,-828 272,-828"/>
+<text text-anchor="middle" x="223.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
 </g>
 <!-- 14&#45;&gt;6 -->
-<g id="edge13" class="edge">
+<g id="edge14" class="edge">
 <title>14&#45;&gt;6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M191.7,-791.88C174.39,-782.55 152.78,-770.92 134.24,-760.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="135.89,-757.85 125.42,-756.19 132.57,-764.01 135.89,-757.85"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M190.6955,-791.8314C173.9138,-782.5368 153.3015,-771.1208 135.3837,-761.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="136.7377,-757.9461 126.294,-756.1628 133.3462,-764.0696 136.7377,-757.9461"/>
 </g>
 <!-- 14&#45;&gt;7 -->
 <g id="edge15" class="edge">
 <title>14&#45;&gt;7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M240.06,-791.7C248.18,-783.22 258.09,-772.86 266.97,-763.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="269.74,-765.75 274.13,-756.1 264.69,-760.91 269.74,-765.75"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M240.4069,-791.8314C248.2813,-783.3694 257.792,-773.1489 266.4013,-763.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="269.1153,-766.1183 273.3654,-756.4133 263.9908,-761.3497 269.1153,-766.1183"/>
 </g>
 <!-- 15 -->
 <g id="node16" class="node">
 <title>15</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M738.5,-828C738.5,-828 628.5,-828 628.5,-828 622.5,-828 616.5,-822 616.5,-816 616.5,-816 616.5,-804 616.5,-804 616.5,-798 622.5,-792 628.5,-792 628.5,-792 738.5,-792 738.5,-792 744.5,-792 750.5,-798 750.5,-804 750.5,-804 750.5,-816 750.5,-816 750.5,-822 744.5,-828 738.5,-828"/>
-<text text-anchor="middle" x="683.5" y="-807.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M738.5,-828C738.5,-828 628.5,-828 628.5,-828 622.5,-828 616.5,-822 616.5,-816 616.5,-816 616.5,-804 616.5,-804 616.5,-798 622.5,-792 628.5,-792 628.5,-792 738.5,-792 738.5,-792 744.5,-792 750.5,-798 750.5,-804 750.5,-804 750.5,-816 750.5,-816 750.5,-822 744.5,-828 738.5,-828"/>
+<text text-anchor="middle" x="683.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
 </g>
 <!-- 15&#45;&gt;7 -->
 <g id="edge16" class="edge">
 <title>15&#45;&gt;7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M616.35,-793.94C613.03,-793.27 609.73,-792.62 606.5,-792 511.49,-773.82 484.72,-772.93 385.68,-756.18"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="385.99,-752.68 375.54,-754.45 384.81,-759.58 385.99,-752.68"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M616.3672,-794.0196C613.0352,-793.3165 609.7323,-792.6391 606.5,-792 511.6028,-773.2369 484.649,-773.3713 385.6674,-756.1726"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="385.9887,-752.6756 375.5344,-754.3954 384.7794,-759.5704 385.9887,-752.6756"/>
 </g>
 <!-- 18 -->
 <g id="node19" class="node">
 <title>18</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M667,-756C667,-756 566,-756 566,-756 560,-756 554,-750 554,-744 554,-744 554,-732 554,-732 554,-726 560,-720 566,-720 566,-720 667,-720 667,-720 673,-720 679,-726 679,-732 679,-732 679,-744 679,-744 679,-750 673,-756 667,-756"/>
-<text text-anchor="middle" x="616.5" y="-735.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M667,-756C667,-756 566,-756 566,-756 560,-756 554,-750 554,-744 554,-744 554,-732 554,-732 554,-726 560,-720 566,-720 566,-720 667,-720 667,-720 673,-720 679,-726 679,-732 679,-732 679,-744 679,-744 679,-750 673,-756 667,-756"/>
+<text text-anchor="middle" x="616.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
 </g>
 <!-- 15&#45;&gt;18 -->
 <g id="edge33" class="edge">
 <title>15&#45;&gt;18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M666.94,-791.7C658.82,-783.22 648.91,-772.86 640.03,-763.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="642.31,-760.91 632.87,-756.1 637.26,-765.75 642.31,-760.91"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M666.5931,-791.8314C658.7187,-783.3694 649.208,-773.1489 640.5987,-763.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="643.0092,-761.3497 633.6346,-756.4133 637.8847,-766.1183 643.0092,-761.3497"/>
 </g>
 <!-- 21 -->
 <g id="node22" class="node">
 <title>21</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1106,-756C1106,-756 1023,-756 1023,-756 1017,-756 1011,-750 1011,-744 1011,-744 1011,-732 1011,-732 1011,-726 1017,-720 1023,-720 1023,-720 1106,-720 1106,-720 1112,-720 1118,-726 1118,-732 1118,-732 1118,-744 1118,-744 1118,-750 1112,-756 1106,-756"/>
-<text text-anchor="middle" x="1064.5" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M1106,-756C1106,-756 1023,-756 1023,-756 1017,-756 1011,-750 1011,-744 1011,-744 1011,-732 1011,-732 1011,-726 1017,-720 1023,-720 1023,-720 1106,-720 1106,-720 1112,-720 1118,-726 1118,-732 1118,-732 1118,-744 1118,-744 1118,-750 1112,-756 1106,-756"/>
+<text text-anchor="middle" x="1064.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
 </g>
 <!-- 15&#45;&gt;21 -->
 <g id="edge39" class="edge">
 <title>15&#45;&gt;21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M750.79,-799.88C813.33,-790.93 909.24,-776.03 1000.82,-756.26"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1001.79,-759.63 1010.82,-754.08 1000.3,-752.8 1001.79,-759.63"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M750.5367,-800.9396C813.1135,-791.9636 909.2168,-776.8572 1000.835,-756.2636"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1001.8553,-759.621 1010.8302,-753.9907 1000.303,-752.7953 1001.8553,-759.621"/>
 </g>
 <!-- 16 -->
 <g id="node17" class="node">
 <title>16</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M615,-540C615,-540 532,-540 532,-540 526,-540 520,-534 520,-528 520,-528 520,-516 520,-516 520,-510 526,-504 532,-504 532,-504 615,-504 615,-504 621,-504 627,-510 627,-516 627,-516 627,-528 627,-528 627,-534 621,-540 615,-540"/>
-<text text-anchor="middle" x="573.5" y="-519.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M615,-540C615,-540 532,-540 532,-540 526,-540 520,-534 520,-528 520,-528 520,-516 520,-516 520,-510 526,-504 532,-504 532,-504 615,-504 615,-504 621,-504 627,-510 627,-516 627,-516 627,-528 627,-528 627,-534 621,-540 615,-540"/>
+<text text-anchor="middle" x="573.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
 </g>
 <!-- 16&#45;&gt;8 -->
 <g id="edge17" class="edge">
 <title>16&#45;&gt;8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M570.36,-503.87C565.93,-479.67 557.79,-435.21 552.52,-406.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="555.89,-405.4 550.65,-396.19 549.01,-406.66 555.89,-405.4"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M570.2071,-503.7623C565.7529,-479.0928 557.7663,-434.8598 552.5507,-405.9731"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="555.9874,-405.3086 550.7662,-396.0896 549.0988,-406.5524 555.9874,-405.3086"/>
 </g>
 <!-- 17&#45;&gt;9 -->
-<g id="edge18" class="edge">
+<g id="edge19" class="edge">
 <title>17&#45;&gt;9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M433.68,-719.88C417.05,-710.64 396.34,-699.13 378.48,-689.21"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="379.88,-685.99 369.44,-684.19 376.48,-692.11 379.88,-685.99"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M432.7049,-719.8314C416.4395,-710.5368 396.4614,-699.1208 379.0949,-689.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="380.7039,-686.0854 370.2849,-684.1628 377.2309,-692.1631 380.7039,-686.0854"/>
 </g>
 <!-- 17&#45;&gt;10 -->
-<g id="edge20" class="edge">
+<g id="edge21" class="edge">
 <title>17&#45;&gt;10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M478.1,-719.7C484.62,-711.39 492.57,-701.28 499.75,-692.14"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="502.63,-694.13 506.06,-684.1 497.13,-689.81 502.63,-694.13"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M478.3788,-719.8314C484.7136,-711.5386 492.3384,-701.557 499.2926,-692.4533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="502.1452,-694.4847 505.4343,-684.4133 496.5825,-690.2353 502.1452,-694.4847"/>
 </g>
 <!-- 18&#45;&gt;9 -->
-<g id="edge19" class="edge">
+<g id="edge18" class="edge">
 <title>18&#45;&gt;9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M553.76,-721.2C513.06,-710.95 459.71,-697.52 416.31,-686.59"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="416.91,-683.13 406.36,-684.09 415.2,-689.92 416.91,-683.13"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M553.7647,-721.752C513.6508,-711.3628 461.2633,-697.7948 418.2129,-686.6451"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="418.8911,-683.2053 408.3329,-684.0862 417.136,-689.9817 418.8911,-683.2053"/>
 </g>
 <!-- 18&#45;&gt;10 -->
-<g id="edge21" class="edge">
+<g id="edge20" class="edge">
 <title>18&#45;&gt;10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M592.52,-719.7C580.19,-710.8 564.98,-699.82 551.65,-690.2"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="553.36,-687.12 543.2,-684.1 549.26,-692.79 553.36,-687.12"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M592.0228,-719.8314C579.9605,-710.8779 565.246,-699.9558 552.2314,-690.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="554.0852,-687.3127 543.9694,-684.1628 549.913,-692.9335 554.0852,-687.3127"/>
 </g>
 <!-- 19&#45;&gt;11 -->
 <g id="edge22" class="edge">
 <title>19&#45;&gt;11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M993.06,-722.69C1013.3,-714.77 1033.59,-702.61 1045.5,-684 1054.13,-670.53 1052.81,-662.23 1045.5,-648 1037.92,-633.24 1024.11,-621.67 1010.45,-613.16"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1011.97,-610 1001.57,-608.01 1008.46,-616.05 1011.97,-610"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M993.0894,-723.1441C1013.3376,-715.0538 1033.6146,-702.7114 1045.5,-684 1054.0788,-670.4943 1052.749,-662.2637 1045.5,-648 1037.9342,-633.1129 1024.1258,-621.3535 1010.4685,-612.6606"/>
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 <!-- 20 -->
 <g id="node21" class="node">
 <title>20</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M1024.5,-684C1024.5,-684 852.5,-684 852.5,-684 846.5,-684 840.5,-678 840.5,-672 840.5,-672 840.5,-660 840.5,-660 840.5,-654 846.5,-648 852.5,-648 852.5,-648 1024.5,-648 1024.5,-648 1030.5,-648 1036.5,-654 1036.5,-660 1036.5,-660 1036.5,-672 1036.5,-672 1036.5,-678 1030.5,-684 1024.5,-684"/>
-<text text-anchor="middle" x="938.5" y="-663.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1024.5,-684C1024.5,-684 852.5,-684 852.5,-684 846.5,-684 840.5,-678 840.5,-672 840.5,-672 840.5,-660 840.5,-660 840.5,-654 846.5,-648 852.5,-648 852.5,-648 1024.5,-648 1024.5,-648 1030.5,-648 1036.5,-654 1036.5,-660 1036.5,-660 1036.5,-672 1036.5,-672 1036.5,-678 1030.5,-684 1024.5,-684"/>
+<text text-anchor="middle" x="938.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
 </g>
 <!-- 19&#45;&gt;20 -->
 <g id="edge36" class="edge">
 <title>19&#45;&gt;20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M932.48,-719.7C933.36,-711.98 934.42,-702.71 935.4,-694.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="938.89,-694.44 936.55,-684.1 931.93,-693.64 938.89,-694.44"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M932.5187,-719.8314C933.3743,-712.131 934.3917,-702.9743 935.3426,-694.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="938.8283,-694.7386 936.4541,-684.4133 931.8711,-693.9656 938.8283,-694.7386"/>
 </g>
 <!-- 26 -->
 <g id="node27" class="node">
 <title>26</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M860,-612C860,-612 765,-612 765,-612 759,-612 753,-606 753,-600 753,-600 753,-588 753,-588 753,-582 759,-576 765,-576 765,-576 860,-576 860,-576 866,-576 872,-582 872,-588 872,-588 872,-600 872,-600 872,-606 866,-612 860,-612"/>
-<text text-anchor="middle" x="812.5" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M860,-612C860,-612 765,-612 765,-612 759,-612 753,-606 753,-600 753,-600 753,-588 753,-588 753,-582 759,-576 765,-576 765,-576 860,-576 860,-576 866,-576 872,-582 872,-588 872,-588 872,-600 872,-600 872,-606 866,-612 860,-612"/>
+<text text-anchor="middle" x="812.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
 </g>
 <!-- 19&#45;&gt;26 -->
-<g id="edge42" class="edge">
+<g id="edge41" class="edge">
 <title>19&#45;&gt;26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M879.36,-719.91C861.77,-711.65 843.51,-699.97 831.5,-684 818.18,-666.29 813.75,-641.27 812.47,-622.27"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="815.96,-621.99 812.04,-612.15 808.97,-622.28 815.96,-621.99"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M878.2953,-719.9048C861.0278,-711.4985 843.2465,-699.7849 831.5,-684 818.2888,-666.2468 813.8129,-641.3423 812.4865,-622.2306"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="815.9733,-621.8532 812.0325,-612.0186 808.9802,-622.1642 815.9733,-621.8532"/>
 </g>
 <!-- 20&#45;&gt;11 -->
-<g id="edge23" class="edge">
+<g id="edge24" class="edge">
 <title>20&#45;&gt;11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M946.66,-647.7C950.41,-639.73 954.95,-630.1 959.12,-621.26"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="962.34,-622.64 963.44,-612.1 956.01,-619.66 962.34,-622.64"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M946.8273,-647.8314C950.473,-639.8771 954.8309,-630.369 958.8627,-621.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="962.0757,-622.9622 963.0606,-612.4133 955.7123,-620.0456 962.0757,-622.9622"/>
 </g>
 <!-- 20&#45;&gt;26 -->
 <g id="edge43" class="edge">
 <title>20&#45;&gt;26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M907.68,-647.88C891.05,-638.64 870.34,-627.13 852.48,-617.21"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="853.88,-613.99 843.44,-612.19 850.48,-620.11 853.88,-613.99"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M906.7049,-647.8314C890.4395,-638.5368 870.4614,-627.1208 853.0949,-617.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="854.7039,-614.0854 844.2849,-612.1628 851.2309,-620.1631 854.7039,-614.0854"/>
 </g>
 <!-- 21&#45;&gt;11 -->
-<g id="edge24" class="edge">
+<g id="edge23" class="edge">
 <title>21&#45;&gt;11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1068.51,-719.91C1071.98,-700.93 1074.61,-670.06 1061.5,-648 1050.33,-629.2 1029.7,-616.35 1011.01,-608.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1012.34,-604.77 1001.76,-604.17 1009.65,-611.24 1012.34,-604.77"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1068.7164,-719.6926C1072.1057,-700.4444 1074.4231,-669.963 1061.5,-648 1050.3537,-629.0567 1029.7305,-615.9763 1011.0356,-607.4394"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1012.3518,-604.1958 1001.7802,-603.4952 1009.6075,-610.6355 1012.3518,-604.1958"/>
 </g>
 <!-- 21&#45;&gt;20 -->
 <g id="edge37" class="edge">
 <title>21&#45;&gt;20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1033.68,-719.88C1017.05,-710.64 996.34,-699.13 978.48,-689.21"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="979.88,-685.99 969.44,-684.19 976.48,-692.11 979.88,-685.99"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1032.7049,-719.8314C1016.4395,-710.5368 996.4614,-699.1208 979.0949,-689.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="980.7039,-686.0854 970.2849,-684.1628 977.2309,-692.1631 980.7039,-686.0854"/>
 </g>
 <!-- 21&#45;&gt;26 -->
-<g id="edge44" class="edge">
+<g id="edge42" class="edge">
 <title>21&#45;&gt;26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1065.91,-719.73C1066.53,-699.7 1064.25,-667.01 1045.5,-648 1033.9,-636.25 946.59,-618.61 882.24,-606.95"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="882.58,-603.46 872.12,-605.14 881.34,-610.35 882.58,-603.46"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1065.9775,-719.8347C1066.5678,-699.5401 1064.1713,-667.0424 1045.5,-648 1033.9274,-636.1973 946.6077,-618.1855 882.2472,-606.255"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="882.5982,-602.7609 872.13,-604.3943 881.3319,-609.6454 882.5982,-602.7609"/>
 </g>
 <!-- 22 -->
 <g id="node23" class="node">
 <title>22</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M971.5,-396C971.5,-396 879.5,-396 879.5,-396 873.5,-396 867.5,-390 867.5,-384 867.5,-384 867.5,-372 867.5,-372 867.5,-366 873.5,-360 879.5,-360 879.5,-360 971.5,-360 971.5,-360 977.5,-360 983.5,-366 983.5,-372 983.5,-372 983.5,-384 983.5,-384 983.5,-390 977.5,-396 971.5,-396"/>
-<text text-anchor="middle" x="925.5" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M971.5,-396C971.5,-396 879.5,-396 879.5,-396 873.5,-396 867.5,-390 867.5,-384 867.5,-384 867.5,-372 867.5,-372 867.5,-366 873.5,-360 879.5,-360 879.5,-360 971.5,-360 971.5,-360 977.5,-360 983.5,-366 983.5,-372 983.5,-372 983.5,-384 983.5,-384 983.5,-390 977.5,-396 971.5,-396"/>
+<text text-anchor="middle" x="925.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
 </g>
 <!-- 22&#45;&gt;12 -->
 <g id="edge25" class="edge">
 <title>22&#45;&gt;12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M905.72,-359.7C895.75,-350.97 883.49,-340.24 872.64,-330.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="874.88,-328.06 865.05,-324.1 870.27,-333.32 874.88,-328.06"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M905.3126,-359.8314C895.6486,-351.1337 883.9204,-340.5783 873.4184,-331.1265"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="875.4553,-328.251 865.6809,-324.1628 870.7725,-333.454 875.4553,-328.251"/>
 </g>
 <!-- 23 -->
 <g id="node24" class="node">
 <title>23</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M459,-900C459,-900 316,-900 316,-900 310,-900 304,-894 304,-888 304,-888 304,-876 304,-876 304,-870 310,-864 316,-864 316,-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="387.5" y="-879.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M459,-900C459,-900 316,-900 316,-900 310,-900 304,-894 304,-888 304,-888 304,-876 304,-876 304,-870 310,-864 316,-864 316,-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="387.5" y="-879.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
 </g>
 <!-- 23&#45;&gt;13 -->
 <g id="edge26" class="edge">
 <title>23&#45;&gt;13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M386.26,-863.7C385.71,-855.98 385.05,-846.71 384.44,-838.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="387.93,-837.83 383.72,-828.1 380.94,-838.33 387.93,-837.83"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M386.2383,-863.8314C385.7035,-856.131 385.0677,-846.9743 384.4734,-838.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="387.9632,-838.1467 383.7787,-828.4133 380.98,-838.6317 387.9632,-838.1467"/>
 </g>
 <!-- 24 -->
 <g id="node25" class="node">
 <title>24</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M274,-900C274,-900 173,-900 173,-900 167,-900 161,-894 161,-888 161,-888 161,-876 161,-876 161,-870 167,-864 173,-864 173,-864 274,-864 274,-864 280,-864 286,-870 286,-876 286,-876 286,-888 286,-888 286,-894 280,-900 274,-900"/>
-<text text-anchor="middle" x="223.5" y="-879.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M274,-900C274,-900 173,-900 173,-900 167,-900 161,-894 161,-888 161,-888 161,-876 161,-876 161,-870 167,-864 173,-864 173,-864 274,-864 274,-864 280,-864 286,-870 286,-876 286,-876 286,-888 286,-888 286,-894 280,-900 274,-900"/>
+<text text-anchor="middle" x="223.5" y="-879.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
 </g>
 <!-- 24&#45;&gt;14 -->
 <g id="edge27" class="edge">
 <title>24&#45;&gt;14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M223.5,-863.7C223.5,-855.98 223.5,-846.71 223.5,-838.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="227,-838.1 223.5,-828.1 220,-838.1 227,-838.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M223.5,-863.8314C223.5,-856.131 223.5,-846.9743 223.5,-838.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="227.0001,-838.4132 223.5,-828.4133 220.0001,-838.4133 227.0001,-838.4132"/>
 </g>
 <!-- 27 -->
 <g id="node28" class="node">
 <title>27</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M586,-828C586,-828 489,-828 489,-828 483,-828 477,-822 477,-816 477,-816 477,-804 477,-804 477,-798 483,-792 489,-792 489,-792 586,-792 586,-792 592,-792 598,-798 598,-804 598,-804 598,-816 598,-816 598,-822 592,-828 586,-828"/>
-<text text-anchor="middle" x="537.5" y="-807.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M586,-828C586,-828 489,-828 489,-828 483,-828 477,-822 477,-816 477,-816 477,-804 477,-804 477,-798 483,-792 489,-792 489,-792 586,-792 586,-792 592,-792 598,-798 598,-804 598,-804 598,-816 598,-816 598,-822 592,-828 586,-828"/>
+<text text-anchor="middle" x="537.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
 </g>
 <!-- 24&#45;&gt;27 -->
 <g id="edge45" class="edge">
 <title>24&#45;&gt;27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M286.2,-865.88C289,-865.24 291.78,-864.61 294.5,-864 368.15,-847.52 389.26,-845.42 467.05,-828.06"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="467.83,-831.47 476.82,-825.87 466.3,-824.64 467.83,-831.47"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M286.1843,-865.9522C288.9922,-865.2826 291.774,-864.6289 294.5,-864 368.0367,-847.0355 389.357,-845.8541 467.0718,-828.0404"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="467.8812,-831.4456 476.836,-825.7833 466.3047,-824.6255 467.8812,-831.4456"/>
 </g>
 <!-- 25 -->
 <g id="node26" class="node">
 <title>25</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M746.5,-900C746.5,-900 620.5,-900 620.5,-900 614.5,-900 608.5,-894 608.5,-888 608.5,-888 608.5,-876 608.5,-876 608.5,-870 614.5,-864 620.5,-864 620.5,-864 746.5,-864 746.5,-864 752.5,-864 758.5,-870 758.5,-876 758.5,-876 758.5,-888 758.5,-888 758.5,-894 752.5,-900 746.5,-900"/>
-<text text-anchor="middle" x="683.5" y="-879.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M746.5,-900C746.5,-900 620.5,-900 620.5,-900 614.5,-900 608.5,-894 608.5,-888 608.5,-888 608.5,-876 608.5,-876 608.5,-870 614.5,-864 620.5,-864 620.5,-864 746.5,-864 746.5,-864 752.5,-864 758.5,-870 758.5,-876 758.5,-876 758.5,-888 758.5,-888 758.5,-894 752.5,-900 746.5,-900"/>
+<text text-anchor="middle" x="683.5" y="-879.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
 </g>
 <!-- 25&#45;&gt;15 -->
 <g id="edge28" class="edge">
 <title>25&#45;&gt;15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M683.5,-863.7C683.5,-855.98 683.5,-846.71 683.5,-838.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="687,-838.1 683.5,-828.1 680,-838.1 687,-838.1"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M683.5,-863.8314C683.5,-856.131 683.5,-846.9743 683.5,-838.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="687.0001,-838.4132 683.5,-828.4133 680.0001,-838.4133 687.0001,-838.4132"/>
 </g>
 <!-- 26&#45;&gt;16 -->
 <g id="edge29" class="edge">
 <title>26&#45;&gt;16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M754.34,-575.97C718.85,-565.57 673.46,-552.28 637.03,-541.61"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="637.59,-538.12 627.01,-538.67 635.62,-544.84 637.59,-538.12"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M752.8067,-576.0171C717.5467,-565.3948 672.9268,-551.9529 637.0192,-541.1355"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="637.722,-537.6919 627.1374,-538.1586 635.7028,-544.3944 637.722,-537.6919"/>
 </g>
 <!-- 27&#45;&gt;17 -->
-<g id="edge30" class="edge">
+<g id="edge31" class="edge">
 <title>27&#45;&gt;17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M519.46,-791.7C510.44,-783.05 499.38,-772.45 489.56,-763.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="491.98,-760.5 482.34,-756.1 487.13,-765.55 491.98,-760.5"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M519.079,-791.8314C510.3471,-783.219 499.7683,-772.7851 490.2577,-763.4048"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="492.4925,-760.6931 482.9151,-756.1628 487.577,-765.6769 492.4925,-760.6931"/>
 </g>
 <!-- 27&#45;&gt;18 -->
 <g id="edge32" class="edge">
 <title>27&#45;&gt;18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M557.03,-791.7C566.88,-782.97 578.99,-772.24 589.7,-762.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="592.03,-765.36 597.2,-756.1 587.39,-760.12 592.03,-765.36"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M557.435,-791.8314C566.9783,-783.1337 578.5599,-772.5783 588.9306,-763.1265"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="591.538,-765.4857 596.5713,-756.1628 586.8228,-760.3121 591.538,-765.4857"/>
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 <!-- 28 -->
 <g id="node29" class="node">
 <title>28</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1104.5,-828C1104.5,-828 1024.5,-828 1024.5,-828 1018.5,-828 1012.5,-822 1012.5,-816 1012.5,-816 1012.5,-804 1012.5,-804 1012.5,-798 1018.5,-792 1024.5,-792 1024.5,-792 1104.5,-792 1104.5,-792 1110.5,-792 1116.5,-798 1116.5,-804 1116.5,-804 1116.5,-816 1116.5,-816 1116.5,-822 1110.5,-828 1104.5,-828"/>
-<text text-anchor="middle" x="1064.5" y="-807.5" font-family="sans" font-size="10.00">create_index_star</text>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M1104.5,-828C1104.5,-828 1024.5,-828 1024.5,-828 1018.5,-828 1012.5,-822 1012.5,-816 1012.5,-816 1012.5,-804 1012.5,-804 1012.5,-798 1018.5,-792 1024.5,-792 1024.5,-792 1104.5,-792 1104.5,-792 1110.5,-792 1116.5,-798 1116.5,-804 1116.5,-804 1116.5,-816 1116.5,-816 1116.5,-822 1110.5,-828 1104.5,-828"/>
+<text text-anchor="middle" x="1064.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
 </g>
 <!-- 28&#45;&gt;19 -->
 <g id="edge34" class="edge">
 <title>28&#45;&gt;19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1031.72,-791.88C1013.87,-782.55 991.6,-770.92 972.5,-760.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="973.89,-757.72 963.41,-756.19 970.65,-763.92 973.89,-757.72"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1030.6861,-791.8314C1013.2293,-782.4516 991.7513,-770.9112 973.1648,-760.9244"/>
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+<g id="edge44" class="edge">
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