From ad3a8e523cf83fcf80b1e17618d3737351399761 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Tue, 10 Mar 2020 12:35:22 +0100
Subject: [PATCH] included tests for ALFA qc
corrected md5sum for config.yaml
remove unnecessary file
---
Snakefile | 4 -
images/dag_test_workflow.svg | 310 +++++++++---------
images/rule_graph.svg | 286 ++++++++--------
tests/test_alfa/expected_output.md5 | 16 +
...reads_paired_Aligned.sortedByCoord.out.bam | Bin 0 -> 2227 bytes
...s_paired_Aligned.sortedByCoord.out.bam.bai | Bin 0 -> 96 bytes
...ed_synthetic_10_reads_paired_Log.final.out | 37 +++
...reads_mate_1_Aligned.sortedByCoord.out.bam | Bin 0 -> 1486 bytes
...s_mate_1_Aligned.sortedByCoord.out.bam.bai | Bin 0 -> 96 bytes
..._1_synthetic_10_reads_mate_1_Log.final.out | 37 +++
.../expected_output.md5 | 8 +
.../expected_output.md5 | 4 +-
.../expected_output.md5 | 2 +-
13 files changed, 399 insertions(+), 305 deletions(-)
create mode 100644 tests/test_alfa/expected_output.md5
create mode 100644 tests/test_alfa/results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam
create mode 100644 tests/test_alfa/results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam.bai
create mode 100644 tests/test_alfa/results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Log.final.out
create mode 100644 tests/test_alfa/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_Aligned.sortedByCoord.out.bam
create mode 100644 tests/test_alfa/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_Aligned.sortedByCoord.out.bam.bai
create mode 100644 tests/test_alfa/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_Log.final.out
diff --git a/Snakefile b/Snakefile
index a51dcf1..5075e82 100644
--- a/Snakefile
+++ b/Snakefile
@@ -678,10 +678,6 @@ rule salmon_quantmerge_transcripts:
#################################################################################
directionality = {"--fr": "fr-firststrand", "--rf": "fr-secondstrand"}
-rename_files = {"fr-firststrand": ("Signal.UniqueMultiple.out.plus.bg",
- "Signal.UniqueMultiple.out.minus.bg"),
- "fr-secondstrand": ("Signal.UniqueMultiple.out.minus.bg",
- "Signal.UniqueMultiple.out.plus.bg")}
rule generate_alfa_index:
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index d3450b8..4c7dde4 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,93 +1,93 @@
<?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 2.40.1 (20161225.0304)
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1976.00 625.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="2113pt" height="625pt"
+ viewBox="0.00 0.00 2112.50 625.00" 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(4 621)">
<title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-621 1972,-621 1972,4 -4,4"/>
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<g id="node1" class="node">
<title>0</title>
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<text text-anchor="middle" x="1480.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
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<g id="node2" class="node">
<title>1</title>
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<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
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<g id="edge1" class="edge">
<title>1->0</title>
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<g id="node3" class="node">
<title>2</title>
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<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
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<g id="edge2" class="edge">
<title>2->0</title>
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<g id="node4" class="node">
<title>3</title>
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<text text-anchor="middle" x="840.5" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<g id="edge3" class="edge">
<title>3->0</title>
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<g id="node5" class="node">
<title>4</title>
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<text text-anchor="middle" x="1341.5" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
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<g id="edge4" class="edge">
<title>4->0</title>
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<g id="node6" class="node">
<title>5</title>
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<text text-anchor="middle" x="1439.5" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
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<g id="edge5" class="edge">
<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1346.4312,-287.8606C1354.648,-253.1867 1371.96,-174.985 1378,-108 1379.4369,-92.0647 1378.2961,-87.9973 1378,-72 1377.8479,-63.7824 1377.5656,-54.865 1377.2602,-46.6892"/>
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<title>6</title>
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<text text-anchor="middle" x="1718.5" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
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<g id="edge6" class="edge">
<title>6->0</title>
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@@ -99,8 +99,8 @@
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<g id="edge7" class="edge">
<title>7->0</title>
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@@ -112,8 +112,8 @@
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<g id="edge8" class="edge">
<title>8->0</title>
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@@ -125,8 +125,8 @@
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<g id="edge9" class="edge">
<title>9->0</title>
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@@ -138,421 +138,421 @@
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<g id="edge10" class="edge">
<title>10->0</title>
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<text text-anchor="middle" x="1556.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
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<g id="edge11" class="edge">
<title>11->0</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1552.37,-287.98C1542.96,-249.41 1518.99,-152.46 1496.5,-72 1494.11,-63.44 1491.36,-54.16 1488.82,-45.79"/>
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<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
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+<path fill="none" stroke="#567bd8" stroke-width="2" d="M1794.5,-252C1794.5,-252 1672.5,-252 1672.5,-252 1666.5,-252 1660.5,-246 1660.5,-240 1660.5,-240 1660.5,-228 1660.5,-228 1660.5,-222 1666.5,-216 1672.5,-216 1672.5,-216 1794.5,-216 1794.5,-216 1800.5,-216 1806.5,-222 1806.5,-228 1806.5,-228 1806.5,-240 1806.5,-240 1806.5,-246 1800.5,-252 1794.5,-252"/>
<text text-anchor="middle" x="1733.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<!-- 11->26 -->
<g id="edge57" class="edge">
<title>11->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1480.2372,-294.1107C1504.718,-283.803 1540.7903,-268.6146 1570.5493,-256.0845"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1572.1086,-259.2256 1579.9668,-252.1193 1569.3922,-252.7742 1572.1086,-259.2256"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1586.53,-293.13C1612.36,-282.91 1650.22,-267.94 1681.05,-255.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1682.35,-258.99 1690.37,-252.06 1679.78,-252.48 1682.35,-258.99"/>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1969.5,-324C1969.5,-324 1933.5,-324 1933.5,-324 1927.5,-324 1921.5,-318 1921.5,-312 1921.5,-312 1921.5,-300 1921.5,-300 1921.5,-294 1927.5,-288 1933.5,-288 1933.5,-288 1969.5,-288 1969.5,-288 1975.5,-288 1981.5,-294 1981.5,-300 1981.5,-300 1981.5,-312 1981.5,-312 1981.5,-318 1975.5,-324 1969.5,-324"/>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1969.5,-324C1969.5,-324 1933.5,-324 1933.5,-324 1927.5,-324 1921.5,-318 1921.5,-312 1921.5,-312 1921.5,-300 1921.5,-300 1921.5,-294 1927.5,-288 1933.5,-288 1933.5,-288 1969.5,-288 1969.5,-288 1975.5,-288 1981.5,-294 1981.5,-300 1981.5,-300 1981.5,-312 1981.5,-312 1981.5,-318 1975.5,-324 1969.5,-324"/>
<text text-anchor="middle" x="1951.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 12->0 -->
<g id="edge12" class="edge">
<title>12->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1793.5802,-303.2749C1731.6888,-296.8917 1587.0545,-279.4064 1547,-252 1507.9241,-225.2632 1463.0834,-108.5619 1433,-72 1424.6772,-61.8849 1414.5713,-51.7549 1405.1936,-43.0465"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1407.2984,-40.23 1397.5428,-36.0973 1402.5919,-45.4116 1407.2984,-40.23"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1921.02,-302.73C1853.83,-297.23 1695.43,-281.45 1651.5,-252 1612.17,-225.64 1567.75,-108.42 1537.5,-72 1529.07,-61.85 1518.77,-51.73 1509.27,-43.1"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1511.33,-40.24 1501.52,-36.22 1506.68,-45.48 1511.33,-40.24"/>
</g>
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M2092.5,-252C2092.5,-252 1970.5,-252 1970.5,-252 1964.5,-252 1958.5,-246 1958.5,-240 1958.5,-240 1958.5,-228 1958.5,-228 1958.5,-222 1964.5,-216 1970.5,-216 1970.5,-216 2092.5,-216 2092.5,-216 2098.5,-216 2104.5,-222 2104.5,-228 2104.5,-228 2104.5,-240 2104.5,-240 2104.5,-246 2098.5,-252 2092.5,-252"/>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M2092.5,-252C2092.5,-252 1970.5,-252 1970.5,-252 1964.5,-252 1958.5,-246 1958.5,-240 1958.5,-240 1958.5,-228 1958.5,-228 1958.5,-222 1964.5,-216 1970.5,-216 1970.5,-216 2092.5,-216 2092.5,-216 2098.5,-216 2104.5,-222 2104.5,-228 2104.5,-228 2104.5,-240 2104.5,-240 2104.5,-246 2098.5,-252 2092.5,-252"/>
<text text-anchor="middle" x="2031.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
<!-- 12->28 -->
<g id="edge59" class="edge">
<title>12->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1841.935,-287.8314C1851.4783,-279.1337 1863.0599,-268.5783 1873.4306,-259.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1876.038,-261.4857 1881.0713,-252.1628 1871.3228,-256.3121 1876.038,-261.4857"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1971.28,-287.7C1981.25,-278.97 1993.51,-268.24 2004.36,-258.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2006.73,-261.32 2011.95,-252.1 2002.12,-256.06 2006.73,-261.32"/>
</g>
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M1760.5,-180C1760.5,-180 1730.5,-180 1730.5,-180 1724.5,-180 1718.5,-174 1718.5,-168 1718.5,-168 1718.5,-156 1718.5,-156 1718.5,-150 1724.5,-144 1730.5,-144 1730.5,-144 1760.5,-144 1760.5,-144 1766.5,-144 1772.5,-150 1772.5,-156 1772.5,-156 1772.5,-168 1772.5,-168 1772.5,-174 1766.5,-180 1760.5,-180"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1760.5,-180C1760.5,-180 1730.5,-180 1730.5,-180 1724.5,-180 1718.5,-174 1718.5,-168 1718.5,-168 1718.5,-156 1718.5,-156 1718.5,-150 1724.5,-144 1730.5,-144 1730.5,-144 1760.5,-144 1760.5,-144 1766.5,-144 1772.5,-150 1772.5,-156 1772.5,-156 1772.5,-168 1772.5,-168 1772.5,-174 1766.5,-180 1760.5,-180"/>
<text text-anchor="middle" x="1745.5" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 13->0 -->
<g id="edge13" class="edge">
<title>13->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1618.8187,-143.7193C1596.6623,-120.4792 1558.9656,-82.1486 1542,-72 1501.167,-47.5743 1447.9824,-32.798 1412.9546,-25.0224"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1413.6528,-21.5926 1403.1417,-22.9218 1412.1875,-28.4376 1413.6528,-21.5926"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1727.32,-143.9C1701.31,-119.54 1655.57,-77.2 1646.5,-72 1605.47,-48.47 1552.65,-33.92 1517.74,-26.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1518.02,-22.63 1507.51,-23.95 1516.55,-29.47 1518.02,-22.63"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1802.5,-108C1802.5,-108 1710.5,-108 1710.5,-108 1704.5,-108 1698.5,-102 1698.5,-96 1698.5,-96 1698.5,-84 1698.5,-84 1698.5,-78 1704.5,-72 1710.5,-72 1710.5,-72 1802.5,-72 1802.5,-72 1808.5,-72 1814.5,-78 1814.5,-84 1814.5,-84 1814.5,-96 1814.5,-96 1814.5,-102 1808.5,-108 1802.5,-108"/>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M1802.5,-108C1802.5,-108 1710.5,-108 1710.5,-108 1704.5,-108 1698.5,-102 1698.5,-96 1698.5,-96 1698.5,-84 1698.5,-84 1698.5,-78 1704.5,-72 1710.5,-72 1710.5,-72 1802.5,-72 1802.5,-72 1808.5,-72 1814.5,-78 1814.5,-84 1814.5,-84 1814.5,-96 1814.5,-96 1814.5,-102 1808.5,-108 1802.5,-108"/>
<text text-anchor="middle" x="1756.5" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 13->15 -->
<g id="edge42" class="edge">
<title>13->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1639.0281,-143.8314C1640.3115,-136.131 1641.8376,-126.9743 1643.2639,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1646.7394,-118.8526 1644.9311,-108.4133 1639.8347,-117.7018 1646.7394,-118.8526"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1748.22,-143.7C1749.43,-135.98 1750.89,-126.71 1752.24,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1755.72,-118.53 1753.81,-108.1 1748.8,-117.44 1755.72,-118.53"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M1887.5,-180C1887.5,-180 1857.5,-180 1857.5,-180 1851.5,-180 1845.5,-174 1845.5,-168 1845.5,-168 1845.5,-156 1845.5,-156 1845.5,-150 1851.5,-144 1857.5,-144 1857.5,-144 1887.5,-144 1887.5,-144 1893.5,-144 1899.5,-150 1899.5,-156 1899.5,-156 1899.5,-168 1899.5,-168 1899.5,-174 1893.5,-180 1887.5,-180"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1887.5,-180C1887.5,-180 1857.5,-180 1857.5,-180 1851.5,-180 1845.5,-174 1845.5,-168 1845.5,-168 1845.5,-156 1845.5,-156 1845.5,-150 1851.5,-144 1857.5,-144 1857.5,-144 1887.5,-144 1887.5,-144 1893.5,-144 1899.5,-150 1899.5,-156 1899.5,-156 1899.5,-168 1899.5,-168 1899.5,-174 1893.5,-180 1887.5,-180"/>
<text text-anchor="middle" x="1872.5" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 14->0 -->
<g id="edge14" class="edge">
<title>14->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1750.5951,-143.9571C1745.6652,-123.1406 1734.4307,-89.5346 1711,-72 1664.433,-37.151 1490.3916,-23.9348 1413.233,-19.7128"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1413.1819,-16.2054 1403.0119,-19.1754 1412.8143,-23.1957 1413.1819,-16.2054"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1868.06,-143.8C1861.78,-123.19 1848.21,-89.29 1823.5,-72 1774.63,-37.82 1596.27,-24.81 1517.89,-20.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1517.68,-17.15 1507.51,-20.14 1517.32,-24.14 1517.68,-17.15"/>
</g>
<!-- 14->15 -->
<g id="edge43" class="edge">
<title>14->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1727.2517,-143.8314C1713.9447,-134.7927 1697.684,-123.7476 1683.3625,-114.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1684.9785,-110.8864 1674.7397,-108.1628 1681.0453,-116.677 1684.9785,-110.8864"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1845.3,-144.59C1829.93,-135.31 1810.5,-123.59 1793.74,-113.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1795.11,-110.21 1784.74,-108.04 1791.49,-116.2 1795.11,-110.21"/>
</g>
<!-- 15->0 -->
<g id="edge15" class="edge">
<title>15->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1594.2616,-75.7751C1540.6047,-61.5718 1459.5833,-40.125 1412.8282,-27.7486"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1413.6767,-24.3528 1403.114,-25.1772 1411.8854,-31.1197 1413.6767,-24.3528"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1698.3,-74.24C1643.75,-60.41 1563.86,-40.14 1517.52,-28.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1518.16,-24.94 1507.61,-25.87 1516.44,-31.73 1518.16,-24.94"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M975.5,-542.5C975.5,-542.5 847.5,-542.5 847.5,-542.5 841.5,-542.5 835.5,-536.5 835.5,-530.5 835.5,-530.5 835.5,-518.5 835.5,-518.5 835.5,-512.5 841.5,-506.5 847.5,-506.5 847.5,-506.5 975.5,-506.5 975.5,-506.5 981.5,-506.5 987.5,-512.5 987.5,-518.5 987.5,-518.5 987.5,-530.5 987.5,-530.5 987.5,-536.5 981.5,-542.5 975.5,-542.5"/>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M975.5,-542.5C975.5,-542.5 847.5,-542.5 847.5,-542.5 841.5,-542.5 835.5,-536.5 835.5,-530.5 835.5,-530.5 835.5,-518.5 835.5,-518.5 835.5,-512.5 841.5,-506.5 847.5,-506.5 847.5,-506.5 975.5,-506.5 975.5,-506.5 981.5,-506.5 987.5,-512.5 987.5,-518.5 987.5,-518.5 987.5,-530.5 987.5,-530.5 987.5,-536.5 981.5,-542.5 975.5,-542.5"/>
<text text-anchor="middle" x="911.5" y="-522" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 16->3 -->
<g id="edge16" class="edge">
<title>16->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M837.5048,-506.4544C825.4956,-479.2448 805,-425.8044 805,-378 805,-378 805,-378 805,-306 805,-265.2729 796.673,-218.7384 790.5061,-189.8595"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="793.9177,-189.0768 788.3512,-180.0621 787.0811,-190.5806 793.9177,-189.0768"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M902.6,-506.22C889.74,-479.63 867.5,-426.73 867.5,-379 867.5,-379 867.5,-379 867.5,-305 867.5,-264.5 856.77,-218.63 848.84,-190.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.1,-188.93 845.96,-180.29 845.37,-190.87 852.1,-188.93"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1481,-468C1481,-468 1380,-468 1380,-468 1374,-468 1368,-462 1368,-456 1368,-456 1368,-444 1368,-444 1368,-438 1374,-432 1380,-432 1380,-432 1481,-432 1481,-432 1487,-432 1493,-438 1493,-444 1493,-444 1493,-456 1493,-456 1493,-462 1487,-468 1481,-468"/>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M1481,-468C1481,-468 1380,-468 1380,-468 1374,-468 1368,-462 1368,-456 1368,-456 1368,-444 1368,-444 1368,-438 1374,-432 1380,-432 1380,-432 1481,-432 1481,-432 1487,-432 1493,-438 1493,-444 1493,-444 1493,-456 1493,-456 1493,-462 1487,-468 1481,-468"/>
<text text-anchor="middle" x="1430.5" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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<!-- 16->19 -->
<g id="edge48" class="edge">
<title>16->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M916.0618,-513.826C1009.3527,-499.6129 1173.3413,-474.629 1266.0609,-460.503"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1266.8217,-463.9276 1276.1804,-458.9613 1265.7673,-457.0074 1266.8217,-463.9276"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M987.52,-512.88C1086.91,-499 1259.83,-474.84 1357.63,-461.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1358.31,-464.62 1367.73,-459.77 1357.34,-457.69 1358.31,-464.62"/>
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<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
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+<path fill="none" stroke="#88d856" stroke-width="2" d="M1082.5,-180C1082.5,-180 964.5,-180 964.5,-180 958.5,-180 952.5,-174 952.5,-168 952.5,-168 952.5,-156 952.5,-156 952.5,-150 958.5,-144 964.5,-144 964.5,-144 1082.5,-144 1082.5,-144 1088.5,-144 1094.5,-150 1094.5,-156 1094.5,-156 1094.5,-168 1094.5,-168 1094.5,-174 1088.5,-180 1082.5,-180"/>
<text text-anchor="middle" x="1023.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 16->24 -->
<g id="edge53" class="edge">
<title>16->24</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="901.6392,-188.0416 908.5408,-180.003 898.1326,-181.9832 901.6392,-188.0416"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-506.15C911.5,-479.02 911.5,-424.91 911.5,-379 911.5,-379 911.5,-379 911.5,-305 911.5,-264.55 906.62,-248.64 930.5,-216 939.95,-203.08 953.57,-192.86 967.48,-184.97"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
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+<path fill="none" stroke="#97d856" stroke-width="2" d="M1049,-252C1049,-252 952,-252 952,-252 946,-252 940,-246 940,-240 940,-240 940,-228 940,-228 940,-222 946,-216 952,-216 952,-216 1049,-216 1049,-216 1055,-216 1061,-222 1061,-228 1061,-228 1061,-240 1061,-240 1061,-246 1055,-252 1049,-252"/>
<text text-anchor="middle" x="1000.5" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
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<!-- 17->3 -->
<g id="edge17" class="edge">
<title>17->3</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="890.08,-180.87 879.51,-180.07 887.27,-187.28 890.08,-180.87"/>
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<!-- 17->4 -->
<g id="edge19" class="edge">
<title>17->4</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1061.04,-217.91C1063.9,-217.25 1066.73,-216.61 1069.5,-216 1128.09,-203.08 1194.15,-190.17 1246.49,-180.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1247.25,-183.75 1256.44,-178.46 1245.96,-176.87 1247.25,-183.75"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
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+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1321.5,-542.5C1321.5,-542.5 1211.5,-542.5 1211.5,-542.5 1205.5,-542.5 1199.5,-536.5 1199.5,-530.5 1199.5,-530.5 1199.5,-518.5 1199.5,-518.5 1199.5,-512.5 1205.5,-506.5 1211.5,-506.5 1211.5,-506.5 1321.5,-506.5 1321.5,-506.5 1327.5,-506.5 1333.5,-512.5 1333.5,-518.5 1333.5,-518.5 1333.5,-530.5 1333.5,-530.5 1333.5,-536.5 1327.5,-542.5 1321.5,-542.5"/>
<text text-anchor="middle" x="1266.5" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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<!-- 18->4 -->
<g id="edge18" class="edge">
<title>18->4</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1226.2621,-190.6608 1229.0183,-180.4307 1220.4841,-186.7091 1226.2621,-190.6608"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-506.15C1266.5,-479.02 1266.5,-424.91 1266.5,-379 1266.5,-379 1266.5,-379 1266.5,-305 1266.5,-259.77 1296.62,-214.85 1318.68,-188"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1321.44,-190.16 1325.23,-180.27 1316.09,-185.64 1321.44,-190.16"/>
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<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
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-<text text-anchor="middle" x="1714" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1877,-468C1877,-468 1794,-468 1794,-468 1788,-468 1782,-462 1782,-456 1782,-456 1782,-444 1782,-444 1782,-438 1788,-432 1794,-432 1794,-432 1877,-432 1877,-432 1883,-432 1889,-438 1889,-444 1889,-444 1889,-456 1889,-456 1889,-462 1883,-468 1877,-468"/>
+<text text-anchor="middle" x="1835.5" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 18->22 -->
<g id="edge51" class="edge">
<title>18->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1241.5172,-515.9175C1344.6577,-501.5281 1551.2037,-472.7122 1653.5953,-458.4273"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1654.3473,-461.8563 1663.7677,-457.0081 1653.38,-454.9235 1654.3473,-461.8563"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1333.73,-514.93C1444.4,-500.83 1663.5,-472.92 1771.81,-459.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.46,-462.56 1781.94,-457.82 1771.58,-455.62 1772.46,-462.56"/>
</g>
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
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+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1226,-180C1226,-180 1125,-180 1125,-180 1119,-180 1113,-174 1113,-168 1113,-168 1113,-156 1113,-156 1113,-150 1119,-144 1125,-144 1125,-144 1226,-144 1226,-144 1232,-144 1238,-150 1238,-156 1238,-156 1238,-168 1238,-168 1238,-174 1232,-180 1226,-180"/>
<text text-anchor="middle" x="1175.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 18->25 -->
<g id="edge55" class="edge">
<title>18->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1172.1264,-506.3912C1160.9959,-479.101 1142,-425.559 1142,-378 1142,-378 1142,-378 1142,-306 1142,-265.1184 1137.5773,-254.1944 1123,-216 1119.4899,-206.8032 1114.5546,-197.3165 1109.652,-188.9099"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1112.5935,-187.0106 1104.414,-180.2765 1106.6088,-190.6416 1112.5935,-187.0106"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1258.81,-506.09C1247.71,-479.33 1228.5,-426.21 1228.5,-379 1228.5,-379 1228.5,-379 1228.5,-305 1228.5,-264.46 1223.88,-253.51 1208.5,-216 1204.7,-206.72 1199.33,-197.22 1194.03,-188.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1196.82,-186.75 1188.38,-180.34 1190.98,-190.62 1196.82,-186.75"/>
</g>
<!-- 19->5 -->
<g id="edge20" class="edge">
<title>19->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1279.1233,-431.902C1262.6378,-423.6643 1246.4852,-412.0564 1237,-396 1228.862,-382.2242 1228.6658,-373.658 1237,-360 1246.0596,-345.1533 1260.6481,-334.2161 1276.1053,-326.2279"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1277.751,-329.3208 1285.2715,-321.8581 1274.7386,-323.0022 1277.751,-329.3208"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1368.25,-431.95C1350.75,-423.98 1333.72,-412.47 1323.5,-396 1315.06,-382.41 1314.85,-373.46 1323.5,-360 1334.35,-343.11 1352.07,-331.53 1370.43,-323.63"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1371.76,-326.87 1379.76,-319.93 1369.18,-320.36 1371.76,-326.87"/>
</g>
<!-- 19->11 -->
<g id="edge34" class="edge">
<title>19->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1386.4292,-431.9219C1403.6028,-423.4959 1421.3206,-411.7651 1433,-396 1446.1732,-378.2186 1450.6522,-353.3165 1451.9895,-334.2128"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1455.4956,-334.1536 1452.4503,-324.0059 1448.5028,-333.8378 1455.4956,-334.1536"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1487.66,-431.93C1506.05,-423.8 1524.91,-412.21 1537.5,-396 1551.1,-378.5 1555.5,-353.46 1556.7,-334.4"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1560.2,-334.36 1557.08,-324.24 1553.21,-334.1 1560.2,-334.36"/>
</g>
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M1516.5,-396C1516.5,-396 1344.5,-396 1344.5,-396 1338.5,-396 1332.5,-390 1332.5,-384 1332.5,-384 1332.5,-372 1332.5,-372 1332.5,-366 1338.5,-360 1344.5,-360 1344.5,-360 1516.5,-360 1516.5,-360 1522.5,-360 1528.5,-366 1528.5,-372 1528.5,-372 1528.5,-384 1528.5,-384 1528.5,-390 1522.5,-396 1516.5,-396"/>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M1516.5,-396C1516.5,-396 1344.5,-396 1344.5,-396 1338.5,-396 1332.5,-390 1332.5,-384 1332.5,-384 1332.5,-372 1332.5,-372 1332.5,-366 1338.5,-360 1344.5,-360 1344.5,-360 1516.5,-360 1516.5,-360 1522.5,-360 1528.5,-366 1528.5,-372 1528.5,-372 1528.5,-384 1528.5,-384 1528.5,-390 1522.5,-396 1516.5,-396"/>
<text text-anchor="middle" x="1430.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="1430.5" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text>
</g>
<!-- 19->20 -->
<g id="edge49" class="edge">
<title>19->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1335,-431.8314C1335,-424.131 1335,-414.9743 1335,-406.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1338.5001,-406.4132 1335,-396.4133 1331.5001,-406.4133 1338.5001,-406.4132"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1430.5,-431.7C1430.5,-423.98 1430.5,-414.71 1430.5,-406.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1434,-406.1 1430.5,-396.1 1427,-406.1 1434,-406.1"/>
</g>
<!-- 20->5 -->
<g id="edge21" class="edge">
<title>20->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1336.7664,-359.8314C1337.515,-352.131 1338.4053,-342.9743 1339.2373,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1342.7256,-334.7051 1340.2098,-324.4133 1335.7585,-334.0276 1342.7256,-334.7051"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1432.72,-359.7C1433.72,-351.98 1434.91,-342.71 1436.01,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1439.5,-334.47 1437.3,-324.1 1432.55,-333.58 1439.5,-334.47"/>
</g>
<!-- 20->11 -->
<g id="edge35" class="edge">
<title>20->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1364.524,-359.8314C1379.8318,-350.4112 1398.6808,-338.8118 1414.9572,-328.7955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1417.014,-331.6395 1423.6962,-323.4177 1413.3453,-325.6779 1417.014,-331.6395"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1461.32,-359.88C1478.2,-350.5 1499.28,-338.79 1517.32,-328.77"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1519.39,-331.62 1526.43,-323.71 1515.99,-325.5 1519.39,-331.62"/>
</g>
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1732.5,-396C1732.5,-396 1596.5,-396 1596.5,-396 1590.5,-396 1584.5,-390 1584.5,-384 1584.5,-384 1584.5,-372 1584.5,-372 1584.5,-366 1590.5,-360 1596.5,-360 1596.5,-360 1732.5,-360 1732.5,-360 1738.5,-360 1744.5,-366 1744.5,-372 1744.5,-372 1744.5,-384 1744.5,-384 1744.5,-390 1738.5,-396 1732.5,-396"/>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1732.5,-396C1732.5,-396 1596.5,-396 1596.5,-396 1590.5,-396 1584.5,-390 1584.5,-384 1584.5,-384 1584.5,-372 1584.5,-372 1584.5,-366 1590.5,-360 1596.5,-360 1596.5,-360 1732.5,-360 1732.5,-360 1738.5,-360 1744.5,-366 1744.5,-372 1744.5,-372 1744.5,-384 1744.5,-384 1744.5,-390 1738.5,-396 1732.5,-396"/>
<text text-anchor="middle" x="1664.5" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 21->5 -->
<g id="edge22" class="edge">
<title>21->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1500.7771,-359.9243C1471.6694,-350.0387 1435.4334,-337.7321 1404.9306,-327.3726"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1405.8392,-323.9849 1395.2448,-324.0831 1403.5881,-330.6131 1405.8392,-323.9849"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1609.75,-359.97C1577.9,-350.06 1537.58,-337.51 1504.17,-327.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1505.09,-323.74 1494.5,-324.11 1503.01,-330.42 1505.09,-323.74"/>
</g>
<!-- 21->6 -->
<g id="edge25" class="edge">
<title>21->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1567.1218,-359.8314C1573.0499,-351.6232 1580.1729,-341.7606 1586.6933,-332.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1589.684,-334.5693 1592.7015,-324.4133 1584.0092,-330.4708 1589.684,-334.5693"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1677.85,-359.7C1684.26,-351.39 1692.06,-341.28 1699.11,-332.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1701.97,-334.16 1705.31,-324.1 1696.43,-329.88 1701.97,-334.16"/>
</g>
<!-- 22->6 -->
<g id="edge23" class="edge">
<title>22->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1700.3217,-431.7623C1681.4139,-406.5518 1647.1827,-360.9103 1625.5714,-332.0952"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1628.3673,-329.9896 1619.5672,-324.0896 1622.7672,-334.1897 1628.3673,-329.9896"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1821.21,-431.84C1812.59,-421.47 1801.4,-407.99 1791.5,-396 1773.79,-374.54 1753.76,-350.1 1739.16,-332.27"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1741.51,-329.61 1732.46,-324.09 1736.09,-334.04 1741.51,-329.61"/>
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<!-- 22->12 -->
<g id="edge36" class="edge">
<title>22->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1764.3807,-439.3338C1805.313,-429.5257 1858.2759,-413.8321 1871,-396 1885.6478,-375.4719 1869.0511,-350.0834 1851.3198,-331.5109"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1889.09,-448.07C1928.28,-444.23 1979.03,-431.98 2005.5,-396 2020.98,-374.96 2001.77,-349.31 1982.1,-330.96"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1984.41,-328.33 1974.61,-324.31 1979.77,-333.57 1984.41,-328.33"/>
</g>
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M1984.5,-396C1984.5,-396 1812.5,-396 1812.5,-396 1806.5,-396 1800.5,-390 1800.5,-384 1800.5,-384 1800.5,-372 1800.5,-372 1800.5,-366 1806.5,-360 1812.5,-360 1812.5,-360 1984.5,-360 1984.5,-360 1990.5,-360 1996.5,-366 1996.5,-372 1996.5,-372 1996.5,-384 1996.5,-384 1996.5,-390 1990.5,-396 1984.5,-396"/>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M1984.5,-396C1984.5,-396 1812.5,-396 1812.5,-396 1806.5,-396 1800.5,-390 1800.5,-384 1800.5,-384 1800.5,-372 1800.5,-372 1800.5,-366 1806.5,-360 1812.5,-360 1812.5,-360 1984.5,-360 1984.5,-360 1990.5,-360 1996.5,-366 1996.5,-372 1996.5,-372 1996.5,-384 1996.5,-384 1996.5,-390 1990.5,-396 1984.5,-396"/>
<text text-anchor="middle" x="1898.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="1898.5" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g>
<!-- 22->23 -->
<g id="edge52" class="edge">
<title>22->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1728.8882,-431.8314C1735.753,-423.454 1744.0301,-413.3531 1751.5511,-404.1749"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1754.2803,-406.3665 1757.9114,-396.4133 1748.8659,-401.9297 1754.2803,-406.3665"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1851.07,-431.7C1858.7,-423.22 1868.02,-412.86 1876.38,-403.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.02,-405.88 1883.11,-396.1 1873.81,-401.2 1879.02,-405.88"/>
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<!-- 23->6 -->
<g id="edge24" class="edge">
<title>23->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1730.8588,-359.8314C1708.5236,-350.2018 1680.9064,-338.295 1657.329,-328.1299"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1854.47,-359.88C1829.53,-350.18 1798.16,-337.98 1771.84,-327.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.98,-324.43 1762.39,-324.07 1770.44,-330.95 1772.98,-324.43"/>
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<!-- 23->12 -->
<g id="edge37" class="edge">
<title>23->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1785.3648,-359.8314C1790.9509,-351.6232 1797.663,-341.7606 1803.8072,-332.7323"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1911.6,-359.7C1917.89,-351.39 1925.55,-341.28 1932.46,-332.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1935.3,-334.19 1938.55,-324.1 1929.72,-329.96 1935.3,-334.19"/>
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<!-- 24->7 -->
<g id="edge26" class="edge">
<title>24->7</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1094.58,-145.82C1097.6,-145.2 1100.58,-144.59 1103.5,-144 1183.8,-127.78 1206.36,-124.57 1290.09,-108.27"/>
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<!-- 24->8 -->
<g id="edge28" class="edge">
<title>24->8</title>
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<title>24->9</title>
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<!-- 24->10 -->
<g id="edge32" class="edge">
<title>24->10</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1065.58,-143.88C1089.3,-134.22 1119.12,-122.09 1144.2,-111.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1145.62,-115.08 1153.56,-108.07 1142.98,-108.6 1145.62,-115.08"/>
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<title>25->7</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1319.07,-114.71 1327.37,-108.11 1316.77,-108.09 1319.07,-114.71"/>
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<g id="edge29" class="edge">
<title>25->8</title>
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<title>25->9</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1056.02,-108.6 1045.44,-108.07 1053.38,-115.08 1056.02,-108.6"/>
</g>
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<title>25->10</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.23,-118.68 1190.61,-108.1 1184.5,-116.76 1191.23,-118.68"/>
</g>
<!-- 26->13 -->
<g id="edge38" class="edge">
<title>26->13</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1736.47,-215.7C1737.79,-207.98 1739.38,-198.71 1740.85,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1744.33,-190.55 1742.57,-180.1 1737.43,-189.37 1744.33,-190.55"/>
</g>
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
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<text text-anchor="middle" x="1882.5" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
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<!-- 27->13 -->
<g id="edge39" class="edge">
<title>27->13</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1848.99,-215.88C1828.65,-205.49 1802.7,-192.22 1781.87,-181.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1783.19,-178.33 1772.69,-176.9 1780.01,-184.56 1783.19,-178.33"/>
</g>
<!-- 27->14 -->
<g id="edge41" class="edge">
<title>27->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1759.9813,-215.8314C1759.1257,-208.131 1758.1083,-198.9743 1757.1574,-190.4166"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1880.03,-215.7C1878.93,-207.98 1877.6,-198.71 1876.37,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.82,-189.51 1874.94,-180.1 1872.89,-190.5 1879.82,-189.51"/>
</g>
<!-- 28->14 -->
<g id="edge40" class="edge">
<title>28->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1863.9057,-215.8314C1841.4302,-204.823 1812.8786,-190.8385 1790.5097,-179.8823"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1992.6,-215.88C1967.01,-204.61 1933.73,-189.96 1908.7,-178.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1910.1,-175.73 1899.54,-174.9 1907.28,-182.14 1910.1,-175.73"/>
</g>
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<g id="node30" class="node">
<title>29</title>
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+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1062,-617C1062,-617 761,-617 761,-617 755,-617 749,-611 749,-605 749,-605 749,-593 749,-593 749,-587 755,-581 761,-581 761,-581 1062,-581 1062,-581 1068,-581 1074,-587 1074,-593 1074,-593 1074,-605 1074,-605 1074,-611 1068,-617 1062,-617"/>
<text text-anchor="middle" x="911.5" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="911.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 29->16 -->
<g id="edge44" class="edge">
<title>29->16</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="849.5001,-552.6265 846,-542.6265 842.5001,-552.6265 849.5001,-552.6265"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-580.82C911.5,-572.42 911.5,-562.12 911.5,-552.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="915,-552.56 911.5,-542.56 908,-552.56 915,-552.56"/>
</g>
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
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<text text-anchor="middle" x="1070.5" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text>
<text text-anchor="middle" x="1070.5" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 30->17 -->
<g id="edge45" class="edge">
<title>30->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M977.5978,-287.8314C969.9585,-279.3694 960.7317,-269.1489 952.3793,-259.8971"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1053.2,-287.7C1044.64,-279.14 1034.16,-268.66 1024.8,-259.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1027.15,-256.7 1017.6,-252.1 1022.2,-261.65 1027.15,-256.7"/>
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<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1188,-252C1188,-252 1091,-252 1091,-252 1085,-252 1079,-246 1079,-240 1079,-240 1079,-228 1079,-228 1079,-222 1085,-216 1091,-216 1091,-216 1188,-216 1188,-216 1194,-216 1200,-222 1200,-228 1200,-228 1200,-240 1200,-240 1200,-246 1194,-252 1188,-252"/>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M1188,-252C1188,-252 1091,-252 1091,-252 1085,-252 1079,-246 1079,-240 1079,-240 1079,-228 1079,-228 1079,-222 1085,-216 1091,-216 1091,-216 1188,-216 1188,-216 1194,-216 1200,-222 1200,-228 1200,-228 1200,-240 1200,-240 1200,-246 1194,-252 1188,-252"/>
<text text-anchor="middle" x="1139.5" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="1139.5" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
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<g id="edge60" class="edge">
<title>30->33</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1087.56,-287.7C1096,-279.14 1106.32,-268.66 1115.54,-259.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.11,-261.68 1122.64,-252.1 1113.13,-256.77 1118.11,-261.68"/>
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<g id="node32" class="node">
<title>31</title>
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+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1423,-617C1423,-617 1110,-617 1110,-617 1104,-617 1098,-611 1098,-605 1098,-605 1098,-593 1098,-593 1098,-587 1104,-581 1110,-581 1110,-581 1423,-581 1423,-581 1429,-581 1435,-587 1435,-593 1435,-593 1435,-605 1435,-605 1435,-611 1429,-617 1423,-617"/>
<text text-anchor="middle" x="1266.5" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1266.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 31->18 -->
<g id="edge46" class="edge">
<title>31->18</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1183.5001,-552.6265 1180,-542.6265 1176.5001,-552.6265 1183.5001,-552.6265"/>
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<g id="node33" class="node">
<title>32</title>
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<text text-anchor="middle" x="1835.5" y="-522" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1835.5" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
@@ -560,32 +560,32 @@
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<g id="edge47" class="edge">
<title>32->19</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.69,-460.55 1493.23,-462.23 1502.46,-467.44 1503.69,-460.55"/>
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<!-- 32->22 -->
<g id="edge50" class="edge">
<title>32->22</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1717.5001,-478.1086 1714,-468.1087 1710.5001,-478.1087 1717.5001,-478.1086"/>
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<!-- 32->27 -->
<g id="edge58" class="edge">
<title>32->27</title>
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<!-- 33->24 -->
<g id="edge54" class="edge">
<title>33->24</title>
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<!-- 33->25 -->
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<title>33->25</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1148.4,-215.7C1152.5,-207.73 1157.45,-198.1 1161.99,-189.26"/>
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</g>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index dcfb1f0..412beab 100644
--- a/images/rule_graph.svg
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<title>2</title>
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<text text-anchor="middle" x="245" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
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<g id="node4" class="node">
<title>3</title>
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<title>3->0</title>
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<g id="node5" class="node">
<title>4</title>
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<title>4->0</title>
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<title>5</title>
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<title>5->0</title>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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<text text-anchor="middle" x="711" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
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<!-- 6->0 -->
<g id="edge2" class="edge">
<title>6->0</title>
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<title>7</title>
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<title>7->0</title>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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<text text-anchor="middle" x="295" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
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<g id="node21" class="node">
<title>20</title>
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<text text-anchor="middle" x="296" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<g id="edge42" class="edge">
<title>8->20</title>
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<title>9</title>
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<text text-anchor="middle" x="299" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
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<g id="node11" class="node">
<title>10</title>
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<text text-anchor="middle" x="386" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
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<title>9->10</title>
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<title>10->0</title>
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<title>11</title>
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<text text-anchor="middle" x="349" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 11->3 -->
-<g id="edge12" class="edge">
+<g id="edge11" class="edge">
<title>11->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M346.846,-503.8314C351.4237,-495.7925 356.9052,-486.1666 361.9588,-477.2918"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="365.1077,-478.8351 367.0147,-468.4133 359.0248,-475.3712 365.1077,-478.8351"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M359.13,-503.7C363.85,-495.64 369.56,-485.89 374.78,-476.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="377.95,-478.5 379.98,-468.1 371.91,-474.96 377.95,-478.5"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M141.5,-468C141.5,-468 40.5,-468 40.5,-468 34.5,-468 28.5,-462 28.5,-456 28.5,-456 28.5,-444 28.5,-444 28.5,-438 34.5,-432 40.5,-432 40.5,-432 141.5,-432 141.5,-432 147.5,-432 153.5,-438 153.5,-444 153.5,-444 153.5,-456 153.5,-456 153.5,-462 147.5,-468 141.5,-468"/>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M141.5,-468C141.5,-468 40.5,-468 40.5,-468 34.5,-468 28.5,-462 28.5,-456 28.5,-456 28.5,-444 28.5,-444 28.5,-438 34.5,-432 40.5,-432 40.5,-432 141.5,-432 141.5,-432 147.5,-432 153.5,-438 153.5,-444 153.5,-444 153.5,-456 153.5,-456 153.5,-462 147.5,-468 141.5,-468"/>
<text text-anchor="middle" x="91" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 11->14 -->
-<g id="edge33" class="edge">
+<g id="edge32" class="edge">
<title>11->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M276.4987,-503.9243C242.8786,-493.7961 200.8229,-481.1266 165.9254,-470.6135"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="166.8698,-467.2427 156.2852,-467.7094 164.8506,-473.9452 166.8698,-467.2427"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M286.22,-503.97C249.25,-493.94 202.32,-481.2 163.75,-470.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="164.19,-467.23 153.62,-467.99 162.35,-473.99 164.19,-467.23"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M820,-468C820,-468 702,-468 702,-468 696,-468 690,-462 690,-456 690,-456 690,-444 690,-444 690,-438 696,-432 702,-432 702,-432 820,-432 820,-432 826,-432 832,-438 832,-444 832,-444 832,-456 832,-456 832,-462 826,-468 820,-468"/>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M820,-468C820,-468 702,-468 702,-468 696,-468 690,-462 690,-456 690,-456 690,-444 690,-444 690,-438 696,-432 702,-432 702,-432 820,-432 820,-432 826,-432 832,-438 832,-444 832,-444 832,-456 832,-456 832,-462 826,-468 820,-468"/>
<text text-anchor="middle" x="761" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 11->18 -->
<g id="edge39" class="edge">
<title>11->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M406.7258,-507.2079C412.3955,-506.0937 418.0402,-505.0111 423.5,-504 517.7823,-486.5405 544.6875,-487.6299 642.2084,-468.1849"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="643.0795,-471.5798 652.1907,-466.1727 641.6962,-464.7179 643.0795,-471.5798"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M425.27,-506.7C430.59,-505.77 435.87,-504.86 441,-504 544.26,-486.72 573.19,-487.17 680.05,-468.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="680.72,-471.55 689.94,-466.33 679.48,-464.66 680.72,-471.55"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M711.5,-540C711.5,-540 614.5,-540 614.5,-540 608.5,-540 602.5,-534 602.5,-528 602.5,-528 602.5,-516 602.5,-516 602.5,-510 608.5,-504 614.5,-504 614.5,-504 711.5,-504 711.5,-504 717.5,-504 723.5,-510 723.5,-516 723.5,-516 723.5,-528 723.5,-528 723.5,-534 717.5,-540 711.5,-540"/>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M711.5,-540C711.5,-540 614.5,-540 614.5,-540 608.5,-540 602.5,-534 602.5,-528 602.5,-528 602.5,-516 602.5,-516 602.5,-510 608.5,-504 614.5,-504 614.5,-504 711.5,-504 711.5,-504 717.5,-504 723.5,-510 723.5,-516 723.5,-516 723.5,-528 723.5,-528 723.5,-534 717.5,-540 711.5,-540"/>
<text text-anchor="middle" x="663" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 12->3 -->
-<g id="edge11" class="edge">
+<g id="edge12" class="edge">
<title>12->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M573.417,-506.1993C537.2316,-495.8194 489.4986,-482.1271 450.2079,-470.8564"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="450.9902,-467.4398 440.4128,-468.0467 449.06,-474.1684 450.9902,-467.4398"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M602.41,-505.46C562.34,-495.19 509.46,-481.63 466.49,-470.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="467.19,-467.18 456.64,-468.09 465.45,-473.96 467.19,-467.18"/>
</g>
<!-- 12->4 -->
<g id="edge14" class="edge">
<title>12->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M610.5837,-503.8314C602.1558,-495.2848 591.959,-484.9443 582.764,-475.6198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="585.1711,-473.0761 575.6575,-468.4133 580.1869,-477.9912 585.1711,-473.0761"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M644.21,-503.7C634.83,-495.05 623.32,-484.45 613.09,-475.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="615.3,-472.3 605.57,-468.1 610.55,-477.45 615.3,-472.3"/>
</g>
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M572,-540C572,-540 462,-540 462,-540 456,-540 450,-534 450,-528 450,-528 450,-516 450,-516 450,-510 456,-504 462,-504 462,-504 572,-504 572,-504 578,-504 584,-510 584,-516 584,-516 584,-528 584,-528 584,-534 578,-540 572,-540"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M572,-540C572,-540 462,-540 462,-540 456,-540 450,-534 450,-528 450,-528 450,-516 450,-516 450,-510 456,-504 462,-504 462,-504 572,-504 572,-504 578,-504 584,-510 584,-516 584,-516 584,-528 584,-528 584,-534 578,-540 572,-540"/>
<text text-anchor="middle" x="517" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 13->4 -->
<g id="edge13" class="edge">
<title>13->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M509.6499,-503.8314C517.1717,-495.3694 526.2565,-485.1489 534.4804,-475.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="537.1049,-478.2127 541.1327,-468.4133 531.873,-473.5621 537.1049,-478.2127"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M534.3,-503.7C542.86,-495.14 553.34,-484.66 562.7,-475.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="565.3,-477.65 569.9,-468.1 560.35,-472.7 565.3,-477.65"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M266.5,-468C266.5,-468 183.5,-468 183.5,-468 177.5,-468 171.5,-462 171.5,-456 171.5,-456 171.5,-444 171.5,-444 171.5,-438 177.5,-432 183.5,-432 183.5,-432 266.5,-432 266.5,-432 272.5,-432 278.5,-438 278.5,-444 278.5,-444 278.5,-456 278.5,-456 278.5,-462 272.5,-468 266.5,-468"/>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M266.5,-468C266.5,-468 183.5,-468 183.5,-468 177.5,-468 171.5,-462 171.5,-456 171.5,-456 171.5,-444 171.5,-444 171.5,-438 177.5,-432 183.5,-432 183.5,-432 266.5,-432 266.5,-432 272.5,-432 278.5,-438 278.5,-444 278.5,-444 278.5,-456 278.5,-456 278.5,-462 272.5,-468 266.5,-468"/>
<text text-anchor="middle" x="225" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 13->17 -->
-<g id="edge37" class="edge">
+<g id="edge36" class="edge">
<title>13->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M431.7413,-506.8859C392.1771,-497.0263 339.5207,-483.5778 284.585,-468.2516"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="285.2411,-464.8006 274.6675,-465.471 283.3513,-471.5407 285.2411,-464.8006"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M449.71,-506.1C406.41,-496.35 348.7,-483.08 288.63,-468.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="289.13,-464.63 278.58,-465.6 287.43,-471.42 289.13,-464.63"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M963.5,-468C963.5,-468 862.5,-468 862.5,-468 856.5,-468 850.5,-462 850.5,-456 850.5,-456 850.5,-444 850.5,-444 850.5,-438 856.5,-432 862.5,-432 862.5,-432 963.5,-432 963.5,-432 969.5,-432 975.5,-438 975.5,-444 975.5,-444 975.5,-456 975.5,-456 975.5,-462 969.5,-468 963.5,-468"/>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M963.5,-468C963.5,-468 862.5,-468 862.5,-468 856.5,-468 850.5,-462 850.5,-456 850.5,-456 850.5,-444 850.5,-444 850.5,-438 856.5,-432 862.5,-432 862.5,-432 963.5,-432 963.5,-432 969.5,-432 975.5,-438 975.5,-444 975.5,-444 975.5,-456 975.5,-456 975.5,-462 969.5,-468 963.5,-468"/>
<text text-anchor="middle" x="913" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 13->19 -->
-<g id="edge41" class="edge">
+<g id="edge40" class="edge">
<title>13->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M555.3795,-505.9594C558.4577,-505.2723 561.5106,-504.6147 564.5,-504 661.4299,-484.0701 689.8687,-489.1188 790.7238,-468.0329"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="791.6611,-471.4119 800.7148,-465.909 790.2056,-464.5649 791.6611,-471.4119"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M584.13,-505.88C587.47,-505.22 590.77,-504.59 594,-504 700.03,-484.59 730.32,-488.52 840.41,-468.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="841.06,-471.45 850.24,-466.16 839.76,-464.57 841.06,-471.45"/>
</g>
<!-- 14->5 -->
-<g id="edge15" class="edge">
+<g id="edge18" class="edge">
<title>14->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M141.5461,-431.9436C165.2169,-421.9205 194.7481,-408.8995 220.5,-396 262.4452,-374.9889 308.9947,-348.2155 340.828,-329.351"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="343.0021,-332.1301 349.8062,-324.0088 339.4227,-326.1144 343.0021,-332.1301"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M144.14,-431.97C172.41,-422.38 207.54,-409.62 238,-396 283.09,-375.85 332.69,-348.32 365.62,-329.24"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="367.57,-332.15 374.45,-324.09 364.05,-326.1 367.57,-332.15"/>
</g>
<!-- 14->8 -->
-<g id="edge23" class="edge">
+<g id="edge25" class="edge">
<title>14->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M60.1998,-431.9669C46.3542,-423.189 32.1642,-411.2027 24.5,-396 17.2973,-381.7129 14.4412,-372.4427 24.5,-360 50.9458,-327.2868 174.4946,-313.4968 238.2346,-308.4803"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="238.5879,-311.9637 248.2966,-307.7223 238.062,-304.9835 238.5879,-311.9637"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M58.47,-431.98C45.21,-423.18 31.3,-411.09 24,-396 17.03,-381.6 13.83,-372.35 24,-360 52.71,-325.13 185.96,-312.88 254.32,-308.84"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="254.91,-312.31 264.7,-308.26 254.52,-305.32 254.91,-312.31"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M217,-396C217,-396 45,-396 45,-396 39,-396 33,-390 33,-384 33,-384 33,-372 33,-372 33,-366 39,-360 45,-360 45,-360 217,-360 217,-360 223,-360 229,-366 229,-372 229,-372 229,-384 229,-384 229,-390 223,-396 217,-396"/>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M217,-396C217,-396 45,-396 45,-396 39,-396 33,-390 33,-384 33,-384 33,-372 33,-372 33,-366 39,-360 45,-360 45,-360 217,-360 217,-360 223,-360 229,-366 229,-372 229,-372 229,-384 229,-384 229,-390 223,-396 217,-396"/>
<text text-anchor="middle" x="131" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 14->15 -->
-<g id="edge34" class="edge">
+<g id="edge35" class="edge">
<title>14->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M103.8086,-431.8314C106.5117,-424.0463 109.7316,-414.7729 112.731,-406.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="116.1327,-407.0081 116.1065,-396.4133 109.52,-404.7119 116.1327,-407.0081"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M100.89,-431.7C105.49,-423.64 111.06,-413.89 116.15,-404.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="119.3,-406.52 121.23,-396.1 113.23,-403.05 119.3,-406.52"/>
</g>
<!-- 15->5 -->
<g id="edge16" class="edge">
<title>15->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M187.0202,-359.9243C225.5374,-349.1335 274.3512,-335.458 313.1825,-324.5792"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="314.1425,-327.9451 322.8275,-321.8771 312.254,-321.2046 314.1425,-327.9451"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M197.19,-359.97C238.54,-349.33 291.69,-335.65 333.62,-324.85"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="334.67,-328.2 343.48,-322.32 332.92,-321.42 334.67,-328.2"/>
</g>
<!-- 15->8 -->
<g id="edge24" class="edge">
<title>15->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M161.3607,-359.8314C185.1682,-348.7006 215.4834,-334.5272 239.0308,-323.5181"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="240.7672,-326.57 248.3436,-319.164 237.8024,-320.2288 240.7672,-326.57"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M171.12,-359.88C196.77,-348.93 229.88,-334.79 255.42,-323.89"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="256.99,-327.03 264.81,-319.89 254.24,-320.59 256.99,-327.03"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M471,-396C471,-396 335,-396 335,-396 329,-396 323,-390 323,-384 323,-384 323,-372 323,-372 323,-366 329,-360 335,-360 335,-360 471,-360 471,-360 477,-360 483,-366 483,-372 483,-372 483,-384 483,-384 483,-390 477,-396 471,-396"/>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M471,-396C471,-396 335,-396 335,-396 329,-396 323,-390 323,-384 323,-384 323,-372 323,-372 323,-366 329,-360 335,-360 335,-360 471,-360 471,-360 477,-360 483,-366 483,-372 483,-372 483,-384 483,-384 483,-390 477,-396 471,-396"/>
<text text-anchor="middle" x="403" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 16->5 -->
-<g id="edge16" class="edge">
+<g id="edge17" class="edge">
<title>16->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M379.5,-359.8314C379.5,-352.131 379.5,-342.9743 379.5,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="383.0001,-334.4132 379.5,-324.4133 376.0001,-334.4133 383.0001,-334.4132"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M403,-359.7C403,-351.98 403,-342.71 403,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="406.5,-334.1 403,-324.1 399.5,-334.1 406.5,-334.1"/>
</g>
<!-- 17->5 -->
-<g id="edge17" class="edge">
+<g id="edge15" class="edge">
<title>17->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M274.6185,-434.3455C277.6155,-433.5227 280.5927,-432.734 283.5,-432 362.1799,-412.1365 411.0864,-458.7832 462.5,-396 472.6372,-383.6211 470.1286,-374.0643 462.5,-360 455.7065,-347.4754 444.6118,-337.4004 432.7131,-329.5017"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="434.3112,-326.376 423.9569,-324.1309 430.6512,-332.343 434.3112,-326.376"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M278.54,-434.21C281.73,-433.43 284.9,-432.69 288,-432 332.93,-421.99 462.41,-431.27 492,-396 502.28,-383.74 499.91,-373.91 492,-360 484.64,-347.04 472.71,-336.92 459.95,-329.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="461.47,-325.99 451.03,-324.15 458.04,-332.1 461.47,-325.99"/>
</g>
<!-- 17->8 -->
-<g id="edge25" class="edge">
+<g id="edge23" class="edge">
<title>17->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M231.0858,-431.7623C240.0333,-406.9846 256.1076,-362.4714 266.5355,-333.5939"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="269.8631,-334.6839 269.9676,-324.0896 263.2792,-332.3064 269.8631,-334.6839"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M233.44,-431.87C245.53,-407.35 267.87,-362.03 282.06,-333.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="285.24,-334.71 286.53,-324.19 278.97,-331.61 285.24,-334.71"/>
</g>
<!-- 17->15 -->
-<g id="edge35" class="edge">
+<g id="edge34" class="edge">
<title>17->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M198.7611,-431.8314C185.9563,-422.7927 170.3091,-411.7476 156.5281,-402.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="158.4188,-399.0703 148.2307,-396.1628 154.382,-404.7891 158.4188,-399.0703"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M201.76,-431.7C189.81,-422.8 175.08,-411.82 162.15,-402.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="164.08,-399.27 153.97,-396.1 159.9,-404.88 164.08,-399.27"/>
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<!-- 18->6 -->
<g id="edge19" class="edge">
<title>18->6</title>
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<!-- 18->7 -->
<g id="edge21" class="edge">
<title>18->7</title>
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<!-- 19->6 -->
<g id="edge20" class="edge">
<title>19->6</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="770.97,-396.08 760.38,-396.11 768.68,-402.69 770.97,-396.08"/>
</g>
<!-- 19->7 -->
<g id="edge22" class="edge">
<title>19->7</title>
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<!-- 20->9 -->
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+<g id="edge26" class="edge">
<title>20->9</title>
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<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
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</g>
<!-- 21->9 -->
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+<g id="edge27" class="edge">
<title>21->9</title>
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<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
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</g>
<!-- 22->11 -->
<g id="edge29" class="edge">
<title>22->11</title>
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</g>
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
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+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M783.5,-612C783.5,-612 682.5,-612 682.5,-612 676.5,-612 670.5,-606 670.5,-600 670.5,-600 670.5,-588 670.5,-588 670.5,-582 676.5,-576 682.5,-576 682.5,-576 783.5,-576 783.5,-576 789.5,-576 795.5,-582 795.5,-588 795.5,-588 795.5,-600 795.5,-600 795.5,-606 789.5,-612 783.5,-612"/>
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<!-- 23->12 -->
<g id="edge30" class="edge">
<title>23->12</title>
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<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
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+<path fill="none" stroke="#d88d56" stroke-width="2" d="M850.5,-540C850.5,-540 753.5,-540 753.5,-540 747.5,-540 741.5,-534 741.5,-528 741.5,-528 741.5,-516 741.5,-516 741.5,-510 747.5,-504 753.5,-504 753.5,-504 850.5,-504 850.5,-504 856.5,-504 862.5,-510 862.5,-516 862.5,-516 862.5,-528 862.5,-528 862.5,-534 856.5,-540 850.5,-540"/>
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<!-- 23->26 -->
<g id="edge44" class="edge">
<title>23->26</title>
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<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
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<g id="edge31" class="edge">
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<g id="node26" class="node">
<title>25</title>
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<title>25->17</title>
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diff --git a/tests/test_alfa/expected_output.md5 b/tests/test_alfa/expected_output.md5
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new file mode 100644
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GIT binary patch
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diff --git a/tests/test_alfa/results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Log.final.out b/tests/test_alfa/results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Log.final.out
new file mode 100644
index 0000000..bd6da57
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+++ b/tests/test_alfa/results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Log.final.out
@@ -0,0 +1,37 @@
+ Started job on | Mar 10 12:04:34
+ Started mapping on | Mar 10 12:04:36
+ Finished on | Mar 10 12:04:36
+ Mapping speed, Million of reads per hour | inf
+
+ Number of input reads | 10
+ Average input read length | 150
+ UNIQUE READS:
+ Uniquely mapped reads number | 10
+ Uniquely mapped reads % | 100.00%
+ Average mapped length | 150.00
+ Number of splices: Total | 0
+ Number of splices: Annotated (sjdb) | 0
+ Number of splices: GT/AG | 0
+ Number of splices: GC/AG | 0
+ Number of splices: AT/AC | 0
+ Number of splices: Non-canonical | 0
+ Mismatch rate per base, % | 0.00%
+ Deletion rate per base | 0.00%
+ Deletion average length | 0.00
+ Insertion rate per base | 0.00%
+ Insertion average length | 0.00
+ MULTI-MAPPING READS:
+ Number of reads mapped to multiple loci | 0
+ % of reads mapped to multiple loci | 0.00%
+ Number of reads mapped to too many loci | 0
+ % of reads mapped to too many loci | 0.00%
+ UNMAPPED READS:
+ Number of reads unmapped: too many mismatches | 0
+ % of reads unmapped: too many mismatches | 0.00%
+ Number of reads unmapped: too short | 0
+ % of reads unmapped: too short | 0.00%
+ Number of reads unmapped: other | 0
+ % of reads unmapped: other | 0.00%
+ CHIMERIC READS:
+ Number of chimeric reads | 0
+ % of chimeric reads | 0.00%
diff --git a/tests/test_alfa/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_Aligned.sortedByCoord.out.bam b/tests/test_alfa/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_Aligned.sortedByCoord.out.bam
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diff --git a/tests/test_alfa/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_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/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_Aligned.sortedByCoord.out.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..bb9718376bfaeeddb2ae1aecc484e09daff86ec3
GIT binary patch
literal 96
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literal 0
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diff --git a/tests/test_alfa/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_Log.final.out b/tests/test_alfa/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_Log.final.out
new file mode 100644
index 0000000..5cd0686
--- /dev/null
+++ b/tests/test_alfa/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_Log.final.out
@@ -0,0 +1,37 @@
+ Started job on | Mar 10 12:04:48
+ Started mapping on | Mar 10 12:04:49
+ Finished on | Mar 10 12:04:49
+ Mapping speed, Million of reads per hour | inf
+
+ Number of input reads | 10
+ Average input read length | 74
+ UNIQUE READS:
+ Uniquely mapped reads number | 10
+ Uniquely mapped reads % | 100.00%
+ Average mapped length | 74.70
+ Number of splices: Total | 0
+ Number of splices: Annotated (sjdb) | 0
+ Number of splices: GT/AG | 0
+ Number of splices: GC/AG | 0
+ Number of splices: AT/AC | 0
+ Number of splices: Non-canonical | 0
+ Mismatch rate per base, % | 0.00%
+ Deletion rate per base | 0.00%
+ Deletion average length | 0.00
+ Insertion rate per base | 0.00%
+ Insertion average length | 0.00
+ MULTI-MAPPING READS:
+ Number of reads mapped to multiple loci | 0
+ % of reads mapped to multiple loci | 0.00%
+ Number of reads mapped to too many loci | 0
+ % of reads mapped to too many loci | 0.00%
+ UNMAPPED READS:
+ Number of reads unmapped: too many mismatches | 0
+ % of reads unmapped: too many mismatches | 0.00%
+ Number of reads unmapped: too short | 0
+ % of reads unmapped: too short | 0.00%
+ Number of reads unmapped: other | 0
+ % of reads unmapped: other | 0.00%
+ CHIMERIC READS:
+ Number of chimeric reads | 0
+ % of chimeric reads | 0.00%
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index f490996..4feedc0 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -87,3 +87,11 @@ ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_s
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ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
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+2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
+a9fdb9b135132dda339b85346525c9c5 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file
diff --git a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
index 7708397..569a4a8 100644
--- a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
@@ -1,2 +1,2 @@
-ba5ae0649d1fb82d94f8d19481498ffd config.yaml
-cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
\ No newline at end of file
+b163e7b06bd9e0a71f2fd1fc4935fea9 config.yaml
+cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
index c24f601..569a4a8 100644
--- a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
@@ -1,2 +1,2 @@
-ba5ae0649d1fb82d94f8d19481498ffd config.yaml
+b163e7b06bd9e0a71f2fd1fc4935fea9 config.yaml
cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
--
GitLab