diff --git a/Snakefile b/Snakefile
index a73c5473dc5213dd9a271b6824052daf49aab1fa..963b69111a69a8a6a31ed3a200ca635f39d7c3c5 100644
--- a/Snakefile
+++ b/Snakefile
@@ -148,7 +148,7 @@ rule create_index_star:
         ),
         sjdbOverhang = "{index_size}",
     singularity:
-        "docker://zavolab/star:2.6.0a"
+        "docker://zavolab/star:2.7.3a-slim"
     threads: 12
     log:
         os.path.join(
@@ -221,7 +221,7 @@ rule create_index_kallisto:
             "{organism}",
         ),
     singularity:
-        "docker://zavolab/kallisto:0.46.1"
+        "docker://zavolab/kallisto:0.46.1-slim"
     log:
         os.path.join(
             config['log_dir'],
@@ -244,7 +244,7 @@ rule extract_transcripts_as_bed12:
             "full_transcripts_protein_coding.bed",
         ),
     singularity:
-        "docker://zavolab/gtf_transcript_type_to_bed12:0.1.0"
+        "docker://zavolab/gtf_transcript_type_to_bed12:0.1.0-slim"
     threads: 1
     log:
         os.path.join(
@@ -299,7 +299,7 @@ rule calculate_TIN_scores:
         )
     threads: 8
     singularity:
-        "docker://zavolab/tin_score_calculation:0.1.0"
+        "docker://zavolab/tin_score_calculation:0.1.0-slim"
     shell:
         "tin_score_calculation.py \
         -i {params.bam} \
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 40592347da7d990db56194885b49803615fede19..7427f6c36460bb53053c9a18d6b0ce9376dde1cd 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,658 +1,366 @@
 <?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">
-<<<<<<< HEAD
 <!-- Generated by graphviz version 2.40.1 (20161225.0304)
  -->
 <!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1626pt" height="414pt"
- viewBox="0.00 0.00 1626.00 414.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1833pt" height="414pt"
+ viewBox="0.00 0.00 1832.50 414.00" 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(4 410)">
 <title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-410 1622,-410 1622,4 -4,4"/>
+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-410 1828.5,-410 1828.5,4 -4,4"/>
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 <g id="node1" class="node">
 <title>0</title>
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-<text text-anchor="middle" x="838" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
-=======
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- -->
-<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1465pt" height="409pt"
- viewBox="0.00 0.00 1464.50 409.00" 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(4 405)">
-<title>snakemake_dag</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-405 1460.5,-405 1460.5,4 -4,4"/>
-<!-- 0 -->
-<g id="node1" class="node">
-<title>0</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M780.5,-36C780.5,-36 750.5,-36 750.5,-36 744.5,-36 738.5,-30 738.5,-24 738.5,-24 738.5,-12 738.5,-12 738.5,-6 744.5,0 750.5,0 750.5,0 780.5,0 780.5,0 786.5,0 792.5,-6 792.5,-12 792.5,-12 792.5,-24 792.5,-24 792.5,-30 786.5,-36 780.5,-36"/>
-<text text-anchor="middle" x="765.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M959.5,-36C959.5,-36 929.5,-36 929.5,-36 923.5,-36 917.5,-30 917.5,-24 917.5,-24 917.5,-12 917.5,-12 917.5,-6 923.5,0 929.5,0 929.5,0 959.5,0 959.5,0 965.5,0 971.5,-6 971.5,-12 971.5,-12 971.5,-24 971.5,-24 971.5,-30 965.5,-36 959.5,-36"/>
+<text text-anchor="middle" x="944.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
 </g>
 <!-- 1 -->
 <g id="node2" class="node">
 <title>1</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M280,-108C280,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 280,-72 280,-72 286,-72 292,-78 292,-84 292,-84 292,-96 292,-96 292,-102 286,-108 280,-108"/>
-<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
-<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-=======
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
-<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
-<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
+<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
+<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
 </g>
 <!-- 1&#45;&gt;0 -->
 <g id="edge1" class="edge">
 <title>1&#45;&gt;0</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M292.0256,-72.9788C295.0432,-72.6476 298.0374,-72.321 301,-72 488.5678,-51.6794 713.2844,-29.9183 800.6774,-21.5536"/>
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-=======
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="728.89,-26.77 738.42,-22.14 728.09,-19.82 728.89,-26.77"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M325.4126,-72.7882C328.1284,-72.5218 330.8259,-72.2589 333.5,-72 550.8548,-50.9569 812.0397,-28.9772 907.3724,-21.0636"/>
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 </g>
 <!-- 2 -->
 <g id="node3" class="node">
 <title>2</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M602,-108C602,-108 322,-108 322,-108 316,-108 310,-102 310,-96 310,-96 310,-84 310,-84 310,-78 316,-72 322,-72 322,-72 602,-72 602,-72 608,-72 614,-78 614,-84 614,-84 614,-96 614,-96 614,-102 608,-108 602,-108"/>
-<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
-<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-=======
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M668,-108C668,-108 355,-108 355,-108 349,-108 343,-102 343,-96 343,-96 343,-84 343,-84 343,-78 349,-72 355,-72 355,-72 668,-72 668,-72 674,-72 680,-78 680,-84 680,-84 680,-96 680,-96 680,-102 674,-108 668,-108"/>
-<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00">fastqc</text>
-<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M668,-108C668,-108 355,-108 355,-108 349,-108 343,-102 343,-96 343,-96 343,-84 343,-84 343,-78 349,-72 355,-72 355,-72 668,-72 668,-72 674,-72 680,-78 680,-84 680,-84 680,-96 680,-96 680,-102 674,-108 668,-108"/>
+<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
+<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
 </g>
 <!-- 2&#45;&gt;0 -->
 <g id="edge2" class="edge">
 <title>2&#45;&gt;0</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M556.3953,-71.9243C635.649,-56.7481 744.6992,-35.8661 801.0125,-25.0827"/>
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-=======
-<path fill="none" stroke="grey" stroke-width="2" d="M573.31,-71.97C621.91,-58.57 687.98,-40.36 728.63,-29.16"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="729.68,-32.5 738.39,-26.47 727.82,-25.75 729.68,-32.5"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M619.9262,-71.9707C713.8941,-56.3456 844.3945,-34.6457 907.4564,-24.1597"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="908.0531,-27.6086 917.3435,-22.5156 906.9048,-20.7034 908.0531,-27.6086"/>
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 <g id="node4" class="node">
 <title>3</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#88d856" stroke-width="2" d="M817.5,-180C817.5,-180 714.5,-180 714.5,-180 708.5,-180 702.5,-174 702.5,-168 702.5,-168 702.5,-156 702.5,-156 702.5,-150 708.5,-144 714.5,-144 714.5,-144 817.5,-144 817.5,-144 823.5,-144 829.5,-150 829.5,-156 829.5,-156 829.5,-168 829.5,-168 829.5,-174 823.5,-180 817.5,-180"/>
-<text text-anchor="middle" x="766" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
-=======
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M556.5,-252C556.5,-252 438.5,-252 438.5,-252 432.5,-252 426.5,-246 426.5,-240 426.5,-240 426.5,-228 426.5,-228 426.5,-222 432.5,-216 438.5,-216 438.5,-216 556.5,-216 556.5,-216 562.5,-216 568.5,-222 568.5,-228 568.5,-228 568.5,-240 568.5,-240 568.5,-246 562.5,-252 556.5,-252"/>
-<text text-anchor="middle" x="497.5" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M916.5,-180C916.5,-180 798.5,-180 798.5,-180 792.5,-180 786.5,-174 786.5,-168 786.5,-168 786.5,-156 786.5,-156 786.5,-150 792.5,-144 798.5,-144 798.5,-144 916.5,-144 916.5,-144 922.5,-144 928.5,-150 928.5,-156 928.5,-156 928.5,-168 928.5,-168 928.5,-174 922.5,-180 916.5,-180"/>
+<text text-anchor="middle" x="857.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
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 <!-- 3&#45;&gt;0 -->
 <g id="edge3" class="edge">
 <title>3&#45;&gt;0</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M732.4003,-143.8076C719.4596,-134.8793 706.092,-122.8246 699,-108 692.0952,-93.5666 689.9641,-85.2042 699,-72 710.8942,-54.619 763.8165,-37.5188 800.8108,-27.3633"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M806.4145,-143.9348C790.4334,-135.5922 774.6105,-123.9115 765.5,-108 757.5498,-94.115 755.959,-84.844 765.5,-72 782.451,-49.1807 859.9959,-32.3091 907.2865,-23.9282"/>
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 <!-- 9 -->
 <g id="node10" class="node">
 <title>9</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M966,-108C966,-108 854,-108 854,-108 848,-108 842,-102 842,-96 842,-96 842,-84 842,-84 842,-78 848,-72 854,-72 854,-72 966,-72 966,-72 972,-72 978,-78 978,-84 978,-84 978,-96 978,-96 978,-102 972,-108 966,-108"/>
-<text text-anchor="middle" x="910" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1112.5,-108C1112.5,-108 960.5,-108 960.5,-108 954.5,-108 948.5,-102 948.5,-96 948.5,-96 948.5,-84 948.5,-84 948.5,-78 954.5,-72 960.5,-72 960.5,-72 1112.5,-72 1112.5,-72 1118.5,-72 1124.5,-78 1124.5,-84 1124.5,-84 1124.5,-96 1124.5,-96 1124.5,-102 1118.5,-108 1112.5,-108"/>
+<text text-anchor="middle" x="1036.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes_tpm</text>
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 <!-- 3&#45;&gt;9 -->
 <g id="edge23" class="edge">
 <title>3&#45;&gt;9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M802.3373,-143.8314C821.3396,-134.3302 844.7758,-122.6121 864.9252,-112.5374"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M902.6693,-143.8314C926.8223,-134.1162 956.7378,-122.0831 982.1556,-111.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="983.6841,-115.017 991.6556,-108.038 981.0718,-108.5227 983.6841,-115.017"/>
 </g>
 <!-- 10 -->
 <g id="node11" class="node">
 <title>10</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M812,-108C812,-108 720,-108 720,-108 714,-108 708,-102 708,-96 708,-96 708,-84 708,-84 708,-78 714,-72 720,-72 720,-72 812,-72 812,-72 818,-72 824,-78 824,-84 824,-84 824,-96 824,-96 824,-102 818,-108 812,-108"/>
-<text text-anchor="middle" x="766" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr</text>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M918,-108C918,-108 787,-108 787,-108 781,-108 775,-102 775,-96 775,-96 775,-84 775,-84 775,-78 781,-72 787,-72 787,-72 918,-72 918,-72 924,-72 930,-78 930,-84 930,-84 930,-96 930,-96 930,-102 924,-108 918,-108"/>
+<text text-anchor="middle" x="852.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr_tpm</text>
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 <!-- 3&#45;&gt;10 -->
 <g id="edge25" class="edge">
 <title>3&#45;&gt;10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M766,-143.8314C766,-136.131 766,-126.9743 766,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="769.5001,-118.4132 766,-108.4133 762.5001,-118.4133 769.5001,-118.4132"/>
-=======
-<path fill="none" stroke="grey" stroke-width="2" d="M529.12,-215.95C568.61,-193.87 637.19,-152.87 688.5,-108 710.51,-88.76 731.97,-63.22 746.62,-44.44"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="749.53,-46.39 752.85,-36.33 743.98,-42.13 749.53,-46.39"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M856.2383,-143.8314C855.7035,-136.131 855.0677,-126.9743 854.4734,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="857.9632,-118.1467 853.7787,-108.4133 850.98,-118.6317 857.9632,-118.1467"/>
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 <!-- 4 -->
 <g id="node5" class="node">
 <title>4</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M953.5,-180C953.5,-180 866.5,-180 866.5,-180 860.5,-180 854.5,-174 854.5,-168 854.5,-168 854.5,-156 854.5,-156 854.5,-150 860.5,-144 866.5,-144 866.5,-144 953.5,-144 953.5,-144 959.5,-144 965.5,-150 965.5,-156 965.5,-156 965.5,-168 965.5,-168 965.5,-174 959.5,-180 953.5,-180"/>
-<text text-anchor="middle" x="910" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
-=======
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-<text text-anchor="middle" x="649.5" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1087,-180C1087,-180 986,-180 986,-180 980,-180 974,-174 974,-168 974,-168 974,-156 974,-156 974,-150 980,-144 986,-144 986,-144 1087,-144 1087,-144 1093,-144 1099,-150 1099,-156 1099,-156 1099,-168 1099,-168 1099,-174 1093,-180 1087,-180"/>
+<text text-anchor="middle" x="1036.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
 </g>
 <!-- 4&#45;&gt;0 -->
 <g id="edge4" class="edge">
 <title>4&#45;&gt;0</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M950.1027,-143.9226C964.4399,-135.2521 979.0139,-123.3548 987,-108 994.3828,-93.8051 996.1862,-85.1001 987,-72 973.8484,-53.245 914.7722,-36.043 875.0749,-26.3079"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="875.7321,-22.8663 865.1917,-23.9392 874.1005,-29.6735 875.7321,-22.8663"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1091.5656,-143.9074C1107.9722,-135.6534 1124.0748,-124.0344 1133.5,-108 1141.608,-94.2065 1143.1351,-84.7736 1133.5,-72 1115.2737,-47.8369 1031.5642,-31.233 981.869,-23.3138"/>
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 <!-- 4&#45;&gt;9 -->
 <g id="edge24" class="edge">
 <title>4&#45;&gt;9</title>
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 <title>7</title>
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 <g id="edge8" class="edge">
 <title>8&#45;&gt;0</title>
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->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
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 <g id="node12" class="node">
 <title>11</title>
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-<text text-anchor="middle" x="775" y="-311" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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+<text text-anchor="middle" x="862.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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 <!-- 11&#45;&gt;3 -->
 <g id="edge11" class="edge">
 <title>11&#45;&gt;3</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M861.8969,-295.2256C861.0372,-269.1777 859.4516,-221.1339 858.4379,-190.4171"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="861.9333,-190.2183 858.1053,-180.3393 854.9371,-190.4493 861.9333,-190.2183"/>
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 <g id="edge15" class="edge">
 <title>11&#45;&gt;5</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M826.3938,-295.4469C804.6539,-284.5769 776.7871,-270.6435 753.6052,-259.0526"/>
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 <g id="node21" class="node">
 <title>20</title>
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-<text text-anchor="middle" x="1194" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
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+<text text-anchor="middle" x="1332.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
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 <!-- 11&#45;&gt;20 -->
 <g id="edge32" class="edge">
 <title>11&#45;&gt;20</title>
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-=======
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-<text text-anchor="middle" x="1025.5" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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-<title>11&#45;&gt;4</title>
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-<title>11&#45;&gt;6</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.86,-261.79 1021.68,-252.06 1018.87,-262.28 1025.86,-261.79"/>
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-<title>19</title>
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-<text text-anchor="middle" x="1320.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
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-<title>11&#45;&gt;19</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.94,-255.72 1266.76,-249.85 1256.21,-248.94 1257.94,-255.72"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1262.404,-260.1697 1271.3665,-254.5195 1260.8367,-253.3474 1262.404,-260.1697"/>
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 <g id="node13" class="node">
 <title>12</title>
-<<<<<<< HEAD
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-<text text-anchor="middle" x="850" y="-245" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-<text text-anchor="middle" x="850" y="-234" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
-<text text-anchor="middle" x="850" y="-223" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1013,-257C1013,-257 898,-257 898,-257 892,-257 886,-251 886,-245 886,-245 886,-228 886,-228 886,-222 892,-216 898,-216 898,-216 1013,-216 1013,-216 1019,-216 1025,-222 1025,-228 1025,-228 1025,-245 1025,-245 1025,-251 1019,-257 1013,-257"/>
+<text text-anchor="middle" x="955.5" y="-245" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<text text-anchor="middle" x="955.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
+<text text-anchor="middle" x="955.5" y="-223" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
 </g>
 <!-- 12&#45;&gt;3 -->
 <g id="edge12" class="edge">
 <title>12&#45;&gt;3</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M928.4616,-215.9453C916.3782,-206.7594 902.0481,-195.8656 889.4399,-186.2809"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="891.5231,-183.468 881.4441,-180.2024 887.2868,-189.0406 891.5231,-183.468"/>
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 <g id="edge14" class="edge">
 <title>12&#45;&gt;4</title>
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-=======
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-<text text-anchor="middle" x="865.5" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="841.42,-258.96 833.38,-252.06 835.37,-262.47 841.42,-258.96"/>
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->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
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 <g id="node14" class="node">
 <title>13</title>
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-<text text-anchor="middle" x="1048" y="-311" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
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+<text text-anchor="middle" x="1171.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
 </g>
 <!-- 13&#45;&gt;4 -->
 <g id="edge13" class="edge">
 <title>13&#45;&gt;4</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1125.4281,-295.4773C1106.9108,-286.3067 1086.6434,-273.5479 1072.5,-257 1056.2035,-237.9328 1046.9034,-210.7334 1041.8556,-190.3208"/>
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 <g id="edge17" class="edge">
 <title>13&#45;&gt;6</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1170.3151,-295.2521C1169.7235,-286.1422 1168.9946,-274.9174 1168.333,-264.7282"/>
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 <!-- 21 -->
 <g id="node22" class="node">
 <title>21</title>
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-<text text-anchor="middle" x="1317" y="-234" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
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+<text text-anchor="middle" x="1466.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
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 <g id="edge34" class="edge">
 <title>13&#45;&gt;21</title>
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-=======
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-<title>13&#45;&gt;7</title>
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->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
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 <!-- 14 -->
 <g id="node15" class="node">
 <title>14</title>
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+<text text-anchor="middle" x="698.5" y="-316.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<text text-anchor="middle" x="698.5" y="-305.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
 </g>
 <!-- 14&#45;&gt;5 -->
 <g id="edge16" class="edge">
 <title>14&#45;&gt;5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M629.7918,-295.2521C631.6847,-286.1422 634.0172,-274.9174 636.1344,-264.7282"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="639.6277,-265.1199 638.2354,-254.6169 632.7741,-263.6957 639.6277,-265.1199"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M700.8699,-295.2521C702.053,-286.1422 703.5107,-274.9174 704.834,-264.7282"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="708.33,-264.9845 706.1472,-254.6169 701.3883,-264.0829 708.33,-264.9845"/>
 </g>
 <!-- 14&#45;&gt;6 -->
 <g id="edge18" class="edge">
 <title>14&#45;&gt;6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M687.5424,-295.4609C691.0701,-294.5881 694.5742,-293.7602 698,-293 796.4385,-271.156 822.5021,-273.3546 922,-257 933.9567,-255.0347 946.5687,-252.9399 958.9664,-250.8683"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="959.5615,-254.3174 968.8465,-249.2147 958.4059,-247.4135 959.5615,-254.3174"/>
-=======
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1230.5,-180C1230.5,-180 1094.5,-180 1094.5,-180 1088.5,-180 1082.5,-174 1082.5,-168 1082.5,-168 1082.5,-156 1082.5,-156 1082.5,-150 1088.5,-144 1094.5,-144 1094.5,-144 1230.5,-144 1230.5,-144 1236.5,-144 1242.5,-150 1242.5,-156 1242.5,-156 1242.5,-168 1242.5,-168 1242.5,-174 1236.5,-180 1230.5,-180"/>
-<text text-anchor="middle" x="1162.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
-</g>
-<!-- 14&#45;&gt;7 -->
-<g id="edge18" class="edge">
-<title>14&#45;&gt;7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1112.61,-143.97C1083.85,-134.14 1047.49,-121.73 1017.21,-111.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1018.2,-108.03 1007.61,-108.11 1015.94,-114.65 1018.2,-108.03"/>
-</g>
-<!-- 14&#45;&gt;8 -->
-<g id="edge20" class="edge">
-<title>14&#45;&gt;8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1162.5,-143.7C1162.5,-135.98 1162.5,-126.71 1162.5,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1166,-118.1 1162.5,-108.1 1159,-118.1 1166,-118.1"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M766.0419,-295.4294C769.9084,-294.5646 773.7479,-293.7471 777.5,-293 890.6171,-270.478 920.4001,-273.8505 1034.5,-257 1046.448,-255.2355 1058.9976,-253.3405 1071.4094,-251.4412"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1071.9669,-254.8967 1081.3198,-249.9194 1070.9044,-247.9778 1071.9669,-254.8967"/>
 </g>
 <!-- 15 -->
 <g id="node16" class="node">
 <title>15</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1250,-180C1250,-180 1084,-180 1084,-180 1078,-180 1072,-174 1072,-168 1072,-168 1072,-156 1072,-156 1072,-150 1078,-144 1084,-144 1084,-144 1250,-144 1250,-144 1256,-144 1262,-150 1262,-156 1262,-156 1262,-168 1262,-168 1262,-174 1256,-180 1250,-180"/>
-<text text-anchor="middle" x="1167" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M1420,-180C1420,-180 1231,-180 1231,-180 1225,-180 1219,-174 1219,-168 1219,-168 1219,-156 1219,-156 1219,-150 1225,-144 1231,-144 1231,-144 1420,-144 1420,-144 1426,-144 1432,-150 1432,-156 1432,-156 1432,-168 1432,-168 1432,-174 1426,-180 1420,-180"/>
+<text text-anchor="middle" x="1325.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
 </g>
 <!-- 15&#45;&gt;7 -->
 <g id="edge19" class="edge">
 <title>15&#45;&gt;7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1167,-143.8314C1167,-136.131 1167,-126.9743 1167,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1170.5001,-118.4132 1167,-108.4133 1163.5001,-118.4133 1170.5001,-118.4132"/>
-=======
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1444.5,-180C1444.5,-180 1272.5,-180 1272.5,-180 1266.5,-180 1260.5,-174 1260.5,-168 1260.5,-168 1260.5,-156 1260.5,-156 1260.5,-150 1266.5,-144 1272.5,-144 1272.5,-144 1444.5,-144 1444.5,-144 1450.5,-144 1456.5,-150 1456.5,-156 1456.5,-156 1456.5,-168 1456.5,-168 1456.5,-174 1450.5,-180 1444.5,-180"/>
-<text text-anchor="middle" x="1358.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-</g>
-<!-- 15&#45;&gt;8 -->
-<g id="edge19" class="edge">
-<title>15&#45;&gt;8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1310.8,-143.97C1283.42,-134.19 1248.84,-121.84 1219.97,-111.52"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1221,-108.18 1210.41,-108.11 1218.65,-114.77 1221,-108.18"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1325.5,-143.8314C1325.5,-136.131 1325.5,-126.9743 1325.5,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1329.0001,-118.4132 1325.5,-108.4133 1322.0001,-118.4133 1329.0001,-118.4132"/>
 </g>
 <!-- 16 -->
 <g id="node17" class="node">
 <title>16</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1413.5,-180C1413.5,-180 1292.5,-180 1292.5,-180 1286.5,-180 1280.5,-174 1280.5,-168 1280.5,-168 1280.5,-156 1280.5,-156 1280.5,-150 1286.5,-144 1292.5,-144 1292.5,-144 1413.5,-144 1413.5,-144 1419.5,-144 1425.5,-150 1425.5,-156 1425.5,-156 1425.5,-168 1425.5,-168 1425.5,-174 1419.5,-180 1413.5,-180"/>
-<text text-anchor="middle" x="1353" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M1598.5,-180C1598.5,-180 1462.5,-180 1462.5,-180 1456.5,-180 1450.5,-174 1450.5,-168 1450.5,-168 1450.5,-156 1450.5,-156 1450.5,-150 1456.5,-144 1462.5,-144 1462.5,-144 1598.5,-144 1598.5,-144 1604.5,-144 1610.5,-150 1610.5,-156 1610.5,-156 1610.5,-168 1610.5,-168 1610.5,-174 1604.5,-180 1598.5,-180"/>
+<text text-anchor="middle" x="1530.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
 </g>
 <!-- 16&#45;&gt;7 -->
 <g id="edge20" class="edge">
 <title>16&#45;&gt;7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1306.0643,-143.8314C1280.8563,-134.0734 1249.6074,-121.977 1223.1209,-111.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1224.1873,-108.384 1213.5981,-108.038 1221.6603,-114.912 1224.1873,-108.384"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1479.0345,-143.9243C1451.0098,-134.0815 1416.1516,-121.8386 1386.736,-111.5073"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1387.5816,-108.0947 1376.9867,-108.0831 1385.2619,-114.6992 1387.5816,-108.0947"/>
 </g>
 <!-- 16&#45;&gt;8 -->
 <g id="edge22" class="edge">
 <title>16&#45;&gt;8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1353,-143.8314C1353,-136.131 1353,-126.9743 1353,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1356.5001,-118.4132 1353,-108.4133 1349.5001,-118.4133 1356.5001,-118.4132"/>
-=======
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M835,-401C835,-401 534,-401 534,-401 528,-401 522,-395 522,-389 522,-389 522,-377 522,-377 522,-371 528,-365 534,-365 534,-365 835,-365 835,-365 841,-365 847,-371 847,-377 847,-377 847,-389 847,-389 847,-395 841,-401 835,-401"/>
-<text text-anchor="middle" x="684.5" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="684.5" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-</g>
-<!-- 16&#45;&gt;9 -->
-<g id="edge21" class="edge">
-<title>16&#45;&gt;9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M686.16,-364.82C686.97,-356.42 687.96,-346.12 688.88,-336.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="692.38,-336.85 689.85,-326.56 685.41,-336.18 692.38,-336.85"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1530.5,-143.8314C1530.5,-136.131 1530.5,-126.9743 1530.5,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1534.0001,-118.4132 1530.5,-108.4133 1527.0001,-118.4133 1534.0001,-118.4132"/>
 </g>
 <!-- 17 -->
 <g id="node18" class="node">
 <title>17</title>
-<<<<<<< HEAD
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1606,-180C1606,-180 1456,-180 1456,-180 1450,-180 1444,-174 1444,-168 1444,-168 1444,-156 1444,-156 1444,-150 1450,-144 1456,-144 1456,-144 1606,-144 1606,-144 1612,-144 1618,-150 1618,-156 1618,-156 1618,-168 1618,-168 1618,-174 1612,-180 1606,-180"/>
-<text text-anchor="middle" x="1531" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1812.5,-180C1812.5,-180 1640.5,-180 1640.5,-180 1634.5,-180 1628.5,-174 1628.5,-168 1628.5,-168 1628.5,-156 1628.5,-156 1628.5,-150 1634.5,-144 1640.5,-144 1640.5,-144 1812.5,-144 1812.5,-144 1818.5,-144 1824.5,-150 1824.5,-156 1824.5,-156 1824.5,-168 1824.5,-168 1824.5,-174 1818.5,-180 1812.5,-180"/>
+<text text-anchor="middle" x="1726.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
 </g>
 <!-- 17&#45;&gt;8 -->
 <g id="edge21" class="edge">
 <title>17&#45;&gt;8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1486.0831,-143.8314C1462.065,-134.1162 1432.3166,-122.0831 1407.0408,-111.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1408.1767,-108.5432 1397.5939,-108.038 1405.5518,-115.0325 1408.1767,-108.5432"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1677.2939,-143.9243C1650.6161,-134.1243 1617.4614,-121.945 1589.4148,-111.6422"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.3199,-108.246 1579.7263,-108.0831 1587.9062,-114.8167 1590.3199,-108.246"/>
 </g>
 <!-- 18 -->
 <g id="node19" class="node">
 <title>18</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M887,-406C887,-406 619,-406 619,-406 613,-406 607,-400 607,-394 607,-394 607,-382 607,-382 607,-376 613,-370 619,-370 619,-370 887,-370 887,-370 893,-370 899,-376 899,-382 899,-382 899,-394 899,-394 899,-400 893,-406 887,-406"/>
-<text text-anchor="middle" x="753" y="-391" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="753" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M993,-406C993,-406 692,-406 692,-406 686,-406 680,-400 680,-394 680,-394 680,-382 680,-382 680,-376 686,-370 692,-370 692,-370 993,-370 993,-370 999,-370 1005,-376 1005,-382 1005,-382 1005,-394 1005,-394 1005,-400 999,-406 993,-406"/>
+<text text-anchor="middle" x="842.5" y="-391" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="842.5" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
 </g>
 <!-- 18&#45;&gt;11 -->
 <g id="edge27" class="edge">
 <title>18&#45;&gt;11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M758.3256,-369.9656C760.8471,-361.427 763.9163,-351.0333 766.731,-341.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="770.1717,-342.2084 769.6472,-331.6265 763.4583,-340.2258 770.1717,-342.2084"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M847.3414,-369.9656C849.6337,-361.427 852.424,-351.0333 854.9827,-341.502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="858.4213,-342.192 857.6338,-331.6265 851.6607,-340.3771 858.4213,-342.192"/>
 </g>
 <!-- 19 -->
 <g id="node20" class="node">
 <title>19</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1209,-406C1209,-406 929,-406 929,-406 923,-406 917,-400 917,-394 917,-394 917,-382 917,-382 917,-376 923,-370 929,-370 929,-370 1209,-370 1209,-370 1215,-370 1221,-376 1221,-382 1221,-382 1221,-394 1221,-394 1221,-400 1215,-406 1209,-406"/>
-<text text-anchor="middle" x="1069" y="-391" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1069" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1348,-406C1348,-406 1035,-406 1035,-406 1029,-406 1023,-400 1023,-394 1023,-394 1023,-382 1023,-382 1023,-376 1029,-370 1035,-370 1035,-370 1348,-370 1348,-370 1354,-370 1360,-376 1360,-382 1360,-382 1360,-394 1360,-394 1360,-400 1354,-406 1348,-406"/>
+<text text-anchor="middle" x="1191.5" y="-391" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1191.5" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
 </g>
 <!-- 19&#45;&gt;13 -->
 <g id="edge28" class="edge">
 <title>19&#45;&gt;13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1063.9165,-369.9656C1061.5096,-361.427 1058.5798,-351.0333 1055.8932,-341.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1059.1914,-340.3018 1053.1095,-331.6265 1052.4539,-342.201 1059.1914,-340.3018"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1186.6586,-369.9656C1184.3663,-361.427 1181.576,-351.0333 1179.0173,-341.502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1182.3393,-340.3771 1176.3662,-331.6265 1175.5787,-342.192 1182.3393,-340.3771"/>
 </g>
 <!-- 20&#45;&gt;15 -->
 <g id="edge29" class="edge">
 <title>20&#45;&gt;15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1187.4641,-218.4656C1184.3366,-209.8361 1180.5224,-199.3119 1177.0382,-189.6981"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1180.2673,-188.3356 1173.5693,-180.1265 1173.6861,-190.7207 1180.2673,-188.3356"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1330.8055,-218.4656C1330.0117,-210.0178 1329.0474,-199.7542 1328.1597,-190.3064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1331.6234,-189.7552 1327.2032,-180.1265 1324.6541,-190.4101 1331.6234,-189.7552"/>
 </g>
 <!-- 21&#45;&gt;17 -->
 <g id="edge30" class="edge">
 <title>21&#45;&gt;17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1365.5599,-219.5948C1396.4256,-208.8495 1436.6502,-194.8461 1469.7072,-183.3379"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1520.0569,-221.1539C1558.6725,-210.089 1611.2447,-195.0251 1653.6717,-182.8681"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1654.7411,-186.2026 1663.3902,-180.0834 1652.8129,-179.4734 1654.7411,-186.2026"/>
 </g>
 <!-- 22 -->
 <g id="node23" class="node">
 <title>22</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M1305.5,-334C1305.5,-334 1204.5,-334 1204.5,-334 1198.5,-334 1192.5,-328 1192.5,-322 1192.5,-322 1192.5,-305 1192.5,-305 1192.5,-299 1198.5,-293 1204.5,-293 1204.5,-293 1305.5,-293 1305.5,-293 1311.5,-293 1317.5,-299 1317.5,-305 1317.5,-305 1317.5,-322 1317.5,-322 1317.5,-328 1311.5,-334 1305.5,-334"/>
-<text text-anchor="middle" x="1255" y="-322" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="1255" y="-311" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1255" y="-300" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1457,-334C1457,-334 1342,-334 1342,-334 1336,-334 1330,-328 1330,-322 1330,-322 1330,-305 1330,-305 1330,-299 1336,-293 1342,-293 1342,-293 1457,-293 1457,-293 1463,-293 1469,-299 1469,-305 1469,-305 1469,-322 1469,-322 1469,-328 1463,-334 1457,-334"/>
+<text text-anchor="middle" x="1399.5" y="-322" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<text text-anchor="middle" x="1399.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
+<text text-anchor="middle" x="1399.5" y="-300" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
 </g>
 <!-- 22&#45;&gt;20 -->
 <g id="edge31" class="edge">
 <title>22&#45;&gt;20</title>
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-=======
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-<title>20</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M1311,-329C1311,-329 1196,-329 1196,-329 1190,-329 1184,-323 1184,-317 1184,-317 1184,-300 1184,-300 1184,-294 1190,-288 1196,-288 1196,-288 1311,-288 1311,-288 1317,-288 1323,-294 1323,-300 1323,-300 1323,-317 1323,-317 1323,-323 1317,-329 1311,-329"/>
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-<text text-anchor="middle" x="1253.5" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1253.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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-<title>20&#45;&gt;18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1235.19,-287.69C1227.2,-279.04 1217.75,-268.81 1209.3,-259.68"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1211.86,-257.29 1202.51,-252.32 1206.72,-262.04 1211.86,-257.29"/>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1300.28,-262.04 1304.49,-252.32 1295.14,-257.29 1300.28,-262.04"/>
->>>>>>> 641f2cbb4025df946ad340a805cb788434b3ba68
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1417.4548,-292.8654C1425.6517,-283.445 1435.4442,-272.191 1444.1159,-262.225"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1446.8544,-264.4097 1450.7783,-254.5683 1441.5736,-259.8148 1446.8544,-264.4097"/>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 5c845f59f06aa16328fa5144f3f22a427f401cc7..9756a86350c383b6c395873d280835c5995c9248 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,243 +1,337 @@
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- viewBox="0.00 0.00 939.50 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1216pt" height="404pt"
+ viewBox="0.00 0.00 1215.50 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
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+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-400 1211.5,-400 1211.5,4 -4,4"/>
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-<text text-anchor="middle" x="281.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M278.5,-36C278.5,-36 248.5,-36 248.5,-36 242.5,-36 236.5,-30 236.5,-24 236.5,-24 236.5,-12 236.5,-12 236.5,-6 242.5,0 248.5,0 248.5,0 278.5,0 278.5,0 284.5,0 290.5,-6 290.5,-12 290.5,-12 290.5,-24 290.5,-24 290.5,-30 284.5,-36 278.5,-36"/>
+<text text-anchor="middle" x="263.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
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-<text text-anchor="middle" x="113.5" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M75.5,-108C75.5,-108 35.5,-108 35.5,-108 29.5,-108 23.5,-102 23.5,-96 23.5,-96 23.5,-84 23.5,-84 23.5,-78 29.5,-72 35.5,-72 35.5,-72 75.5,-72 75.5,-72 81.5,-72 87.5,-78 87.5,-84 87.5,-84 87.5,-96 87.5,-96 87.5,-102 81.5,-108 75.5,-108"/>
+<text text-anchor="middle" x="55.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
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+<g id="edge1" class="edge">
+<title>1&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M87.602,-75.5405C90.594,-74.3037 93.5933,-73.1048 96.5,-72 140.5109,-55.2724 192.2328,-39.0651 226.324,-28.844"/>
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-<text text-anchor="middle" x="188.5" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M147.5,-108C147.5,-108 117.5,-108 117.5,-108 111.5,-108 105.5,-102 105.5,-96 105.5,-96 105.5,-84 105.5,-84 105.5,-78 111.5,-72 117.5,-72 117.5,-72 147.5,-72 147.5,-72 153.5,-72 159.5,-78 159.5,-84 159.5,-84 159.5,-96 159.5,-96 159.5,-102 153.5,-108 147.5,-108"/>
+<text text-anchor="middle" x="132.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="252.891,-44.9145 258.776,-36.1043 248.681,-39.3217 252.891,-44.9145"/>
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+<title>2&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M159.6433,-75.0816C179.3158,-64.2692 206.1157,-49.5395 227.5636,-37.7513"/>
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-<text text-anchor="middle" x="63.5" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<g id="node4" class="node">
+<title>3</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M428.5,-180C428.5,-180 310.5,-180 310.5,-180 304.5,-180 298.5,-174 298.5,-168 298.5,-168 298.5,-156 298.5,-156 298.5,-150 304.5,-144 310.5,-144 310.5,-144 428.5,-144 428.5,-144 434.5,-144 440.5,-150 440.5,-156 440.5,-156 440.5,-168 440.5,-168 440.5,-174 434.5,-180 428.5,-180"/>
+<text text-anchor="middle" x="369.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
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-<path fill="none" stroke="grey" stroke-width="2" d="M90.8692,-215.973C124.885,-193.92 183.454,-152.942 224.5,-108 241.966,-88.8761 257.5,-63.7838 267.923,-45.1186"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="271.035,-46.723 272.753,-36.2684 264.89,-43.3697 271.035,-46.723"/>
+<g id="edge2" class="edge">
+<title>3&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M326.0408,-143.997C310.0967,-135.3368 293.3209,-123.4271 282.5,-108 269.8693,-89.9927 265.3299,-65.3098 263.8314,-46.3472"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="267.3177,-46.0003 263.2709,-36.2088 260.3284,-46.3868 267.3177,-46.0003"/>
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+<!-- 8 -->
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M629.5,-108C629.5,-108 477.5,-108 477.5,-108 471.5,-108 465.5,-102 465.5,-96 465.5,-96 465.5,-84 465.5,-84 465.5,-78 471.5,-72 477.5,-72 477.5,-72 629.5,-72 629.5,-72 635.5,-72 641.5,-78 641.5,-84 641.5,-84 641.5,-96 641.5,-96 641.5,-102 635.5,-108 629.5,-108"/>
+<text text-anchor="middle" x="553.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes_tpm</text>
+</g>
+<!-- 3&#45;&gt;8 -->
+<g id="edge22" class="edge">
+<title>3&#45;&gt;8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M415.931,-143.8314C440.868,-134.0734 471.7809,-121.977 497.9826,-111.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="499.3659,-114.9414 507.4029,-108.038 496.8151,-108.4227 499.3659,-114.9414"/>
+</g>
+<!-- 9 -->
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M435,-108C435,-108 304,-108 304,-108 298,-108 292,-102 292,-96 292,-96 292,-84 292,-84 292,-78 298,-72 304,-72 304,-72 435,-72 435,-72 441,-72 447,-78 447,-84 447,-84 447,-96 447,-96 447,-102 441,-108 435,-108"/>
+<text text-anchor="middle" x="369.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr_tpm</text>
+</g>
+<!-- 3&#45;&gt;9 -->
+<g id="edge24" class="edge">
+<title>3&#45;&gt;9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M369.5,-143.8314C369.5,-136.131 369.5,-126.9743 369.5,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="373.0001,-118.4132 369.5,-108.4133 366.0001,-118.4133 373.0001,-118.4132"/>
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-<text text-anchor="middle" x="200.5" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<g id="node5" class="node">
+<title>4</title>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M572,-180C572,-180 471,-180 471,-180 465,-180 459,-174 459,-168 459,-168 459,-156 459,-156 459,-150 465,-144 471,-144 471,-144 572,-144 572,-144 578,-144 584,-150 584,-156 584,-156 584,-168 584,-168 584,-174 578,-180 572,-180"/>
+<text text-anchor="middle" x="521.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
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+<title>4&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M581.6631,-143.9748C611.1402,-133.8034 642.0932,-120.6327 650.5,-108 659.3642,-94.6799 661.0029,-84.0702 650.5,-72 627.6671,-45.7599 393.0238,-26.9047 300.6114,-20.4437"/>
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+</g>
+<!-- 4&#45;&gt;8 -->
+<g id="edge21" class="edge">
+<title>4&#45;&gt;8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M529.575,-143.8314C533.1102,-135.8771 537.336,-126.369 541.2456,-117.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="544.4532,-118.9729 545.3163,-108.4133 538.0565,-116.1299 544.4532,-118.9729"/>
+</g>
+<!-- 4&#45;&gt;9 -->
+<g id="edge23" class="edge">
+<title>4&#45;&gt;9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M483.144,-143.8314C462.9956,-134.2874 438.1248,-122.5065 416.7917,-112.4013"/>
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-<text text-anchor="middle" x="357.5" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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+<title>5</title>
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+<text text-anchor="middle" x="93.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="294.265,-44.4845 287.62,-36.2325 287.668,-46.8272 294.265,-44.4845"/>
+<g id="edge3" class="edge">
+<title>5&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M107.7017,-215.9555C137.7641,-177.7585 207.9332,-88.6025 242.9143,-44.1559"/>
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-<text text-anchor="middle" x="533.5" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M363.5,-252C363.5,-252 217.5,-252 217.5,-252 211.5,-252 205.5,-246 205.5,-240 205.5,-240 205.5,-228 205.5,-228 205.5,-222 211.5,-216 217.5,-216 217.5,-216 363.5,-216 363.5,-216 369.5,-216 375.5,-222 375.5,-228 375.5,-228 375.5,-240 375.5,-240 375.5,-246 369.5,-252 363.5,-252"/>
+<text text-anchor="middle" x="290.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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 <!-- 6&#45;&gt;0 -->
-<g id="edge2" class="edge"><title>6&#45;&gt;0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="304.545,-41.8464 295.633,-36.1164 299.026,-46.1532 304.545,-41.8464"/>
+<g id="edge4" class="edge">
+<title>6&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M285.5956,-215.8118C279.2989,-191.4728 268.6861,-146.863 264.5,-108 262.2861,-87.4468 262.0933,-64.1016 262.4239,-46.3388"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="265.923,-46.4174 262.6759,-36.3324 258.9252,-46.2411 265.923,-46.4174"/>
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 <!-- 7 -->
-<g id="node8" class="node"><title>7</title>
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-<text text-anchor="middle" x="573.5" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M883,-108C883,-108 788,-108 788,-108 782,-108 776,-102 776,-96 776,-96 776,-84 776,-84 776,-78 782,-72 788,-72 788,-72 883,-72 883,-72 889,-72 895,-78 895,-84 895,-84 895,-96 895,-96 895,-102 889,-108 883,-108"/>
+<text text-anchor="middle" x="835.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
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 <!-- 7&#45;&gt;0 -->
-<g id="edge1" class="edge"><title>7&#45;&gt;0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M517.199,-75.5033C458.593,-61.4537 368.502,-39.8566 318.378,-27.8405"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="319.151,-24.4268 308.61,-25.4991 317.519,-31.2339 319.151,-24.4268"/>
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-<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M360.5,-324C360.5,-324 248.5,-324 248.5,-324 242.5,-324 236.5,-318 236.5,-312 236.5,-312 236.5,-300 236.5,-300 236.5,-294 242.5,-288 248.5,-288 248.5,-288 360.5,-288 360.5,-288 366.5,-288 372.5,-294 372.5,-300 372.5,-300 372.5,-312 372.5,-312 372.5,-318 366.5,-324 360.5,-324"/>
-<text text-anchor="middle" x="304.5" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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-<!-- 8&#45;&gt;3 -->
-<g id="edge9" class="edge"><title>8&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M245.853,-287.966C211.594,-278.015 168.184,-265.406 132.314,-254.987"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="132.989,-251.539 122.41,-252.111 131.037,-258.261 132.989,-251.539"/>
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-<!-- 8&#45;&gt;5 -->
-<g id="edge13" class="edge"><title>8&#45;&gt;5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M317.601,-287.697C323.891,-279.389 331.547,-269.277 338.465,-260.141"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="341.304,-262.19 344.55,-252.104 335.723,-257.964 341.304,-262.19"/>
-</g>
-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M728,-252C728,-252 639,-252 639,-252 633,-252 627,-246 627,-240 627,-240 627,-228 627,-228 627,-222 633,-216 639,-216 639,-216 728,-216 728,-216 734,-216 740,-222 740,-228 740,-228 740,-240 740,-240 740,-246 734,-252 728,-252"/>
-<text text-anchor="middle" x="683.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
-</g>
-<!-- 8&#45;&gt;17 -->
-<g id="edge24" class="edge"><title>8&#45;&gt;17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M372.886,-289.657C375.793,-289.082 378.674,-288.527 381.5,-288 482.647,-269.141 511.799,-272.997 616.656,-252.052"/>
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-</g>
-<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M156,-324C156,-324 71,-324 71,-324 65,-324 59,-318 59,-312 59,-312 59,-300 59,-300 59,-294 65,-288 71,-288 71,-288 156,-288 156,-288 162,-288 168,-294 168,-300 168,-300 168,-312 168,-312 168,-318 162,-324 156,-324"/>
-<text text-anchor="middle" x="113.5" y="-303.5" font-family="sans" font-size="10.00">create_index_salmon</text>
-</g>
-<!-- 9&#45;&gt;3 -->
-<g id="edge8" class="edge"><title>9&#45;&gt;3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M101.14,-287.697C95.2672,-279.474 88.1309,-269.483 81.6576,-260.421"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="84.3779,-258.207 75.7174,-252.104 78.6817,-262.276 84.3779,-258.207"/>
-</g>
-<!-- 9&#45;&gt;4 -->
-<g id="edge11" class="edge"><title>9&#45;&gt;4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M135.006,-287.697C145.963,-278.881 159.446,-268.032 171.325,-258.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="173.645,-261.1 179.242,-252.104 169.256,-255.646 173.645,-261.1"/>
+<g id="edge9" class="edge">
+<title>7&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M775.9047,-82.4985C658,-67.6573 397.9937,-34.9293 300.9757,-22.7172"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="301.1269,-19.2087 290.768,-21.4323 300.2526,-26.1539 301.1269,-19.2087"/>
+</g>
+<!-- 8&#45;&gt;0 -->
+<g id="edge5" class="edge">
+<title>8&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M480.6951,-71.9243C423.4138,-57.7027 345.9515,-38.4707 300.6911,-27.2337"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="301.2742,-23.7722 290.7254,-24.7594 299.5874,-30.566 301.2742,-23.7722"/>
+</g>
+<!-- 9&#45;&gt;0 -->
+<g id="edge8" class="edge">
+<title>9&#45;&gt;0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M342.7517,-71.8314C329.4447,-62.7927 313.184,-51.7476 298.8625,-42.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="300.4785,-38.8864 290.2397,-36.1628 296.5453,-44.677 300.4785,-38.8864"/>
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 <!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M624.5,-324C624.5,-324 528.5,-324 528.5,-324 522.5,-324 516.5,-318 516.5,-312 516.5,-312 516.5,-300 516.5,-300 516.5,-294 522.5,-288 528.5,-288 528.5,-288 624.5,-288 624.5,-288 630.5,-288 636.5,-294 636.5,-300 636.5,-300 636.5,-312 636.5,-312 636.5,-318 630.5,-324 624.5,-324"/>
-<text text-anchor="middle" x="576.5" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 10&#45;&gt;4 -->
-<g id="edge10" class="edge"><title>10&#45;&gt;4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M516.363,-289.831C513.372,-289.187 510.405,-288.573 507.5,-288 403.939,-267.586 373.787,-273.413 266.048,-251.975"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="266.572,-248.51 256.077,-249.958 265.184,-255.371 266.572,-248.51"/>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M467.5,-324C467.5,-324 339.5,-324 339.5,-324 333.5,-324 327.5,-318 327.5,-312 327.5,-312 327.5,-300 327.5,-300 327.5,-294 333.5,-288 339.5,-288 339.5,-288 467.5,-288 467.5,-288 473.5,-288 479.5,-294 479.5,-300 479.5,-300 479.5,-312 479.5,-312 479.5,-318 473.5,-324 467.5,-324"/>
+<text text-anchor="middle" x="403.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 10&#45;&gt;3 -->
+<g id="edge11" class="edge">
+<title>10&#45;&gt;3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M400.0453,-287.9951C396.4678,-269.7725 390.5612,-240.8217 384.5,-216 382.4324,-207.5329 379.9752,-198.3795 377.6542,-190.0569"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="381.0174,-189.0876 374.9259,-180.4191 374.2821,-190.9943 381.0174,-189.0876"/>
+</g>
+<!-- 10&#45;&gt;5 -->
+<g id="edge15" class="edge">
+<title>10&#45;&gt;5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M327.2684,-288.2946C283.0085,-278.0149 227.0782,-265.0246 181.0234,-254.328"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="181.5861,-250.8656 171.0536,-252.0124 180.0024,-257.6841 181.5861,-250.8656"/>
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-<!-- 10&#45;&gt;6 -->
-<g id="edge14" class="edge"><title>10&#45;&gt;6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M565.871,-287.697C560.872,-279.559 554.809,-269.689 549.288,-260.701"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="552.223,-258.793 544.007,-252.104 546.259,-262.457 552.223,-258.793"/>
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-<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M843,-252C843,-252 770,-252 770,-252 764,-252 758,-246 758,-240 758,-240 758,-228 758,-228 758,-222 764,-216 770,-216 770,-216 843,-216 843,-216 849,-216 855,-222 855,-228 855,-228 855,-240 855,-240 855,-246 849,-252 843,-252"/>
-<text text-anchor="middle" x="806.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M753,-252C753,-252 652,-252 652,-252 646,-252 640,-246 640,-240 640,-240 640,-228 640,-228 640,-222 646,-216 652,-216 652,-216 753,-216 753,-216 759,-216 765,-222 765,-228 765,-228 765,-240 765,-240 765,-246 759,-252 753,-252"/>
+<text text-anchor="middle" x="702.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
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-<!-- 10&#45;&gt;18 -->
-<g id="edge25" class="edge"><title>10&#45;&gt;18</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="749.158,-256.111 757.705,-249.851 747.119,-249.414 749.158,-256.111"/>
+<!-- 10&#45;&gt;19 -->
+<g id="edge29" class="edge">
+<title>10&#45;&gt;19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M478.5644,-287.9243C524.8179,-276.7863 583.8339,-262.5751 629.6681,-251.5381"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="630.6316,-254.9062 639.5343,-249.1623 628.9927,-248.1008 630.6316,-254.9062"/>
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 <!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M486.5,-324C486.5,-324 402.5,-324 402.5,-324 396.5,-324 390.5,-318 390.5,-312 390.5,-312 390.5,-300 390.5,-300 390.5,-294 396.5,-288 402.5,-288 402.5,-288 486.5,-288 486.5,-288 492.5,-288 498.5,-294 498.5,-300 498.5,-300 498.5,-312 498.5,-312 498.5,-318 492.5,-324 486.5,-324"/>
-<text text-anchor="middle" x="444.5" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
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-<!-- 11&#45;&gt;5 -->
-<g id="edge12" class="edge"><title>11&#45;&gt;5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M422.994,-287.697C412.037,-278.881 398.554,-268.032 386.675,-258.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="388.744,-255.646 378.758,-252.104 384.355,-261.1 388.744,-255.646"/>
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-<!-- 11&#45;&gt;6 -->
-<g id="edge15" class="edge"><title>11&#45;&gt;6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M466.5,-287.697C477.709,-278.881 491.502,-268.032 503.654,-258.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="506.057,-261.038 511.753,-252.104 501.729,-255.535 506.057,-261.038"/>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M541,-252C541,-252 444,-252 444,-252 438,-252 432,-246 432,-240 432,-240 432,-228 432,-228 432,-222 438,-216 444,-216 444,-216 541,-216 541,-216 547,-216 553,-222 553,-228 553,-228 553,-240 553,-240 553,-246 547,-252 541,-252"/>
+<text text-anchor="middle" x="492.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+</g>
+<!-- 11&#45;&gt;3 -->
+<g id="edge10" class="edge">
+<title>11&#45;&gt;3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M461.4619,-215.8314C445.7295,-206.6221 426.4389,-195.3301 409.5956,-185.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="410.9265,-182.1941 400.5282,-180.1628 407.3902,-188.2352 410.9265,-182.1941"/>
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+<!-- 11&#45;&gt;4 -->
+<g id="edge12" class="edge">
+<title>11&#45;&gt;4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M499.8179,-215.8314C502.9876,-207.9617 506.77,-198.5712 510.2813,-189.8533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="513.5939,-190.9968 514.0835,-180.4133 507.1008,-188.3815 513.5939,-190.9968"/>
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-<g id="node13" class="node"><title>12</title>
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-<text text-anchor="middle" x="480.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
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-<!-- 12&#45;&gt;7 -->
-<g id="edge17" class="edge"><title>12&#45;&gt;7</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="544.891,-116.915 550.776,-108.104 540.681,-111.322 544.891,-116.915"/>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M636.5,-324C636.5,-324 526.5,-324 526.5,-324 520.5,-324 514.5,-318 514.5,-312 514.5,-312 514.5,-300 514.5,-300 514.5,-294 520.5,-288 526.5,-288 526.5,-288 636.5,-288 636.5,-288 642.5,-288 648.5,-294 648.5,-300 648.5,-300 648.5,-312 648.5,-312 648.5,-318 642.5,-324 636.5,-324"/>
+<text text-anchor="middle" x="581.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+</g>
+<!-- 12&#45;&gt;4 -->
+<g id="edge13" class="edge">
+<title>12&#45;&gt;4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M580.0081,-287.6774C577.9477,-268.9522 573.1883,-239.3838 562.5,-216 558.0225,-206.2043 551.508,-196.5125 544.9846,-188.1017"/>
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+<!-- 12&#45;&gt;6 -->
+<g id="edge16" class="edge">
+<title>12&#45;&gt;6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M514.3733,-289.3913C472.3963,-279.0053 418.0143,-265.5499 373.3607,-254.5016"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="373.9537,-251.0429 363.4057,-252.0385 372.2724,-257.838 373.9537,-251.0429"/>
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+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M878,-252C878,-252 795,-252 795,-252 789,-252 783,-246 783,-240 783,-240 783,-228 783,-228 783,-222 789,-216 795,-216 795,-216 878,-216 878,-216 884,-216 890,-222 890,-228 890,-228 890,-240 890,-240 890,-246 884,-252 878,-252"/>
+<text text-anchor="middle" x="836.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+</g>
+<!-- 12&#45;&gt;20 -->
+<g id="edge31" class="edge">
+<title>12&#45;&gt;20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M646.7594,-287.9111C681.7622,-278.169 725.8822,-265.8263 772.9686,-252.4263"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="774.0824,-255.7483 782.7407,-249.6422 772.1644,-249.0162 774.0824,-255.7483"/>
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-<g id="node14" class="node"><title>13</title>
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-<g id="edge18" class="edge"><title>13&#45;&gt;7</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="606.319,-111.322 596.224,-108.104 602.109,-116.915 606.319,-111.322"/>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M220,-324C220,-324 123,-324 123,-324 117,-324 111,-318 111,-312 111,-312 111,-300 111,-300 111,-294 117,-288 123,-288 123,-288 220,-288 220,-288 226,-288 232,-294 232,-300 232,-300 232,-312 232,-312 232,-318 226,-324 220,-324"/>
+<text text-anchor="middle" x="171.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+</g>
+<!-- 13&#45;&gt;5 -->
+<g id="edge14" class="edge">
+<title>13&#45;&gt;5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M151.8173,-287.8314C142.3949,-279.1337 130.9599,-268.5783 120.7204,-259.1265"/>
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+<path fill="none" stroke="#569ad8" stroke-width="2" d="M981.5,-180C981.5,-180 845.5,-180 845.5,-180 839.5,-180 833.5,-174 833.5,-168 833.5,-168 833.5,-156 833.5,-156 833.5,-150 839.5,-144 845.5,-144 845.5,-144 981.5,-144 981.5,-144 987.5,-144 993.5,-150 993.5,-156 993.5,-156 993.5,-168 993.5,-168 993.5,-174 987.5,-180 981.5,-180"/>
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+<!-- 15&#45;&gt;7 -->
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+<g id="node17" class="node">
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+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1195.5,-180C1195.5,-180 1023.5,-180 1023.5,-180 1017.5,-180 1011.5,-174 1011.5,-168 1011.5,-168 1011.5,-156 1011.5,-156 1011.5,-150 1017.5,-144 1023.5,-144 1023.5,-144 1195.5,-144 1195.5,-144 1201.5,-144 1207.5,-150 1207.5,-156 1207.5,-156 1207.5,-168 1207.5,-168 1207.5,-174 1201.5,-180 1195.5,-180"/>
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+<text text-anchor="middle" x="403.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
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+<title>18&#45;&gt;12</title>
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+<!-- 21 -->
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+<!-- 21&#45;&gt;20 -->
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 07abc1e88f490702b8f19812ced038eced8d2308..d5d5e83a3b30bee1d6eaa6e469da8c174e0b214f 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -8,23 +8,23 @@ d0826904b8afa45352906ad9591f2bfb  results/star_indexes/homo_sapiens/75/STAR_inde
 8d3291e6bcdbe9902fbd7c887494173f  results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
 83ea3c15ab782b5c55bfaefda8e7aad8  results/star_indexes/homo_sapiens/75/STAR_index/exonGeTrInfo.tab
 bad9d837f9a988694cc7080ee6d2997a  results/star_indexes/homo_sapiens/75/STAR_index/exonInfo.tab
-97e90abd8df5b91bd0b0f94dbeb66fbd  results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
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 00dda17b3c3983873d1474e9a758d6e6  results/star_indexes/homo_sapiens/75/STAR_index/Genome
 c0d91c3af633d9439bfd0160d11efe4d  results/star_indexes/homo_sapiens/75/STAR_index/SA
 27884e419e42a7c8b3b2f49543de0260  results/star_indexes/homo_sapiens/75/STAR_index/SAindex
 bae93882f9148a6c55816b733c32a3a2  results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
-ea36f062eedc7f54ceffea2b635a25a8  results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
+875030141343fca11f0b5aa1a37e1b66  results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
 ea36f062eedc7f54ceffea2b635a25a8  results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
-59c4082523c0279740fa0452871dea4b  results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
+65e794aa5096551254af18a678d02264  results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
 500dd49da40b16799aba62aa5cf239ba  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq
 e90e31db1ce51d930645eb74ff70d21b  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate2.fastq
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 e90e31db1ce51d930645eb74ff70d21b  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq
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 42741852cc110a151580bb3bb5180fc0  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
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@@ -33,10 +33,10 @@ e4c1a39967ec9547a2e4c71c97982ee0  results/paired_end/synthetic_10_reads_paired_s
 69b70e3f561b749bf10b186dd2480a8a  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
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 5d406428979b59abf760b9be8b1877e2  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc.fo
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@@ -57,10 +57,10 @@ d41d8cd98f00b204e9800998ecf8427e  results/paired_end/synthetic_10_reads_paired_s
 12ac6d56ed50ab74ce16a4d618612847  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.remove_adapters_mate1.fastq
 12ac6d56ed50ab74ce16a4d618612847  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.remove_polya_mate1.fastq
 d41d8cd98f00b204e9800998ecf8427e  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_SJ.out.tab
-69042457ef7ec3f401153e8503408ad4  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
+6c5d2ffd046e24384a7557aa9be0fdfd  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
 c0df759ceab72ea4b1a560f991fe6497  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
 a7530faae728593900da23fca4bea97a  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
-fe6c1c9343d91f5413c8319ccd72b5d5  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
+310130cbb8bbb6517f37ea0ff6586d43  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
 42741852cc110a151580bb3bb5180fc0  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
 8b34217d5fd931966d9007a658570e67  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
 848396c145d2157f34bbf86757f51abe  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index ec650632cdc438ecc8e41e2e2e50e9e5193d95da..5f10636dd17051d88c85320ad28e309cfdd337d1 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -3,6 +3,7 @@
 # Tear down test environment
 cleanup () {
     rc=$?
+    rm -rf .fontconfig/
     rm -rf .java/
     rm -rf .snakemake/
     rm -rf logs/
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 00aacd131ccff4c3cc1896a2db91a852c57ea841..f67878a809a4b71dc56ce2c40fc28153c0947faf 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -3,6 +3,7 @@
 # Tear down test environment
 cleanup () {
     rc=$?
+    rm -rf .fontconfig/
     rm -rf .java/
     rm -rf .snakemake/
     rm -rf logs/
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index da8ed992c58cc225765baaa53ddc7987ce425b6f..a0d87d17e597f1fe3bc9fcf692807e4cf8b2273e 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -11,7 +11,7 @@ rule pe_fastqc:
     threads:
         2
     singularity:
-        "docker://zavolab/fastqc:0.11.8"
+        "docker://zavolab/fastqc:0.11.9-slim"
     log:
         os.path.join(config["log_dir"],"paired_end", "{sample}", "fastqc.log")
     shell:
@@ -48,7 +48,7 @@ rule pe_remove_adapters_cutadapt:
         adapter_5_mate2 = lambda wildcards:
             samples_table.loc[wildcards.sample, 'fq2_5p']
     singularity:
-        "docker://zavolab/cutadapt:1.16"
+        "docker://zavolab/cutadapt:1.16-slim"
     threads: 8
     log:
         os.path.join( config["log_dir"], "paired_end", "{sample}", "remove_adapters_cutadapt.log")
@@ -99,7 +99,7 @@ rule pe_remove_polya_cutadapt:
         polya_3_mate2 = lambda wildcards:
             samples_table.loc[wildcards.sample, 'fq2_polya'],
     singularity:
-        "docker://zavolab/cutadapt:1.16"
+        "docker://zavolab/cutadapt:1.16-slim"
     threads: 8
     log:
         os.path.join( config["log_dir"], "paired_end", "{sample}", "remove_polya_cutadapt.log")
@@ -176,7 +176,7 @@ rule pe_map_genome_star:
             samples_table.loc[wildcards.sample, "pass_mode"]
 
     singularity:
-        "docker://zavolab/star:2.6.0a"
+        "docker://zavolab/star:2.7.3a-slim"
 
     threads: 12
 
@@ -224,7 +224,7 @@ rule pe_index_genomic_alignment_samtools:
             "map_genome",
             "{sample}_Aligned.sortedByCoord.out.bam.bai"),
     singularity:
-        "docker://zavolab/samtools:1.8"
+        "docker://zavolab/samtools:1.10-slim"
     log:
         os.path.join( config["log_dir"], "paired_end", "{sample}", "index_genomic_alignment_samtools.log")
     shell:
@@ -326,7 +326,7 @@ rule pe_genome_quantification_kallisto:
         directionality = lambda wildcards:
             samples_table.loc[wildcards.sample, "kallisto_directionality"]
     singularity:
-        "docker://zavolab/kallisto:0.46.1"
+        "docker://zavolab/kallisto:0.46.1-slim"
     threads:    8
     log:
         os.path.join(config["log_dir"], "paired_end", "{sample}", "genome_quantification_kallisto.log")
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 3b365d89ab9c40979a266e9ca52e719c504c8bb2..aa0ed104eb0abf83407ac7faa85103407fd8fb5b 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -8,7 +8,7 @@ rule fastqc:
     params:
         seqmode= lambda wildcards: samples_table.loc[wildcards.sample, "seqmode"]
     singularity:
-        "docker://zavolab/fastqc:0.11.8"
+        "docker://zavolab/fastqc:0.11.9-slim"
     log:
         os.path.join(config["log_dir"], "single_end", "{sample}", "fastqc.log")
     shell:
@@ -31,7 +31,7 @@ rule remove_adapters_cutadapt:
             samples_table.loc[wildcards.sample, 'fq1_5p']
 
     singularity:
-        "docker://zavolab/cutadapt:1.16"
+        "docker://zavolab/cutadapt:1.16-slim"
     threads: 8
     log:
         os.path.join(config["log_dir"], "single_end", "{sample}", "remove_adapters_cutadapt.log")
@@ -58,7 +58,7 @@ rule remove_polya_cutadapt:
         polya_3 = lambda wildcards: 
             samples_table.loc[wildcards.sample, "fq1_polya"]
     singularity:
-        "docker://zavolab/cutadapt:1.16"
+        "docker://zavolab/cutadapt:1.16-slim"
     threads: 8
     log:
         os.path.join(config["log_dir"], "single_end", "{sample}", "remove_polya_cutadapt.log")
@@ -112,9 +112,9 @@ rule map_genome_star:
         soft_clip = lambda wildcards:
                 samples_table.loc[wildcards.sample, "soft_clip"],
         pass_mode = lambda wildcards:
-                samples_table.loc[wildcards.sample, "pass_mode"],        
+                samples_table.loc[wildcards.sample, "pass_mode"],
     singularity:
-        "docker://zavolab/star:2.6.0a"
+        "docker://zavolab/star:2.7.3a-slim"
     threads: 12
     log:
         os.path.join(config["log_dir"], "single_end", "{sample}", "map_genome_star.log")
@@ -157,7 +157,7 @@ rule index_genomic_alignment_samtools:
             "map_genome", 
             "{sample}_Aligned.sortedByCoord.out.bam.bai")
     singularity:
-        "docker://zavolab/samtools:1.8"
+        "docker://zavolab/samtools:1.10-slim"
     threads: 1
     log:
         os.path.join(config["log_dir"], "single_end", "{sample}", "index_genomic_alignment_samtools.log")
@@ -252,7 +252,7 @@ rule genome_quantification_kallisto:
     log:
         os.path.join(config["log_dir"], "single_end", "{sample}", "genome_quantification_kallisto.log.log")
     singularity:
-        "docker://zavolab/kallisto:0.46.1"
+        "docker://zavolab/kallisto:0.46.1-slim"
     shell:
         "(kallisto quant \
         -i {input.index} \