From 81c4c7b4739af3cdf77b5c4e73470d9589e1c0c1 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Wed, 11 Mar 2020 14:53:37 +0100
Subject: [PATCH] replaced synthetic test by new one.
---
images/dag_test_workflow.svg | 68 +++++------
images/rule_graph.svg | 106 +++++++++---------
tests/test_alfa/expected_output.md5 | 46 +++++---
tests/test_alfa/input_files/config.yaml | 9 ++
.../input_files/homo_sapiens/quick_start.gtf | 6 +
tests/test_alfa/input_files/samples.tsv | 5 +
...us_antisense_Aligned.sortedByCoord.out.bam | Bin 0 -> 767 bytes
...ntisense_Aligned.sortedByCoord.out.bam.bai | Bin 0 -> 96 bytes
..._minus_sense_Aligned.sortedByCoord.out.bam | Bin 0 -> 767 bytes
...us_sense_Aligned.sortedByCoord.out.bam.bai | Bin 0 -> 96 bytes
...us_antisense_Aligned.sortedByCoord.out.bam | Bin 0 -> 768 bytes
...ntisense_Aligned.sortedByCoord.out.bam.bai | Bin 0 -> 96 bytes
...n_plus_sense_Aligned.sortedByCoord.out.bam | Bin 0 -> 768 bytes
...us_sense_Aligned.sortedByCoord.out.bam.bai | Bin 0 -> 96 bytes
...reads_paired_Aligned.sortedByCoord.out.bam | Bin 2227 -> 0 bytes
...s_paired_Aligned.sortedByCoord.out.bam.bai | Bin 96 -> 0 bytes
...ed_synthetic_10_reads_paired_Log.final.out | 37 ------
...reads_mate_1_Aligned.sortedByCoord.out.bam | Bin 1486 -> 0 bytes
...s_mate_1_Aligned.sortedByCoord.out.bam.bai | Bin 96 -> 0 bytes
..._1_synthetic_10_reads_mate_1_Log.final.out | 37 ------
.../75/STAR_index/chrNameLength.txt | 2 +-
tests/test_alfa/test.sh | 6 +-
22 files changed, 140 insertions(+), 182 deletions(-)
create mode 100644 tests/test_alfa/input_files/config.yaml
create mode 100644 tests/test_alfa/input_files/homo_sapiens/quick_start.gtf
create mode 100644 tests/test_alfa/input_files/samples.tsv
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam.bai
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam.bai
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam
create mode 100644 tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai
delete 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
delete 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
delete 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
delete 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
delete 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
delete 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/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 4c7dde4..720c5f0 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -12,13 +12,13 @@
<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M1495.5,-36C1495.5,-36 1465.5,-36 1465.5,-36 1459.5,-36 1453.5,-30 1453.5,-24 1453.5,-24 1453.5,-12 1453.5,-12 1453.5,-6 1459.5,0 1465.5,0 1465.5,0 1495.5,0 1495.5,0 1501.5,0 1507.5,-6 1507.5,-12 1507.5,-12 1507.5,-24 1507.5,-24 1507.5,-30 1501.5,-36 1495.5,-36"/>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M1495.5,-36C1495.5,-36 1465.5,-36 1465.5,-36 1459.5,-36 1453.5,-30 1453.5,-24 1453.5,-24 1453.5,-12 1453.5,-12 1453.5,-6 1459.5,0 1465.5,0 1465.5,0 1495.5,0 1495.5,0 1501.5,0 1507.5,-6 1507.5,-12 1507.5,-12 1507.5,-24 1507.5,-24 1507.5,-30 1501.5,-36 1495.5,-36"/>
<text text-anchor="middle" x="1480.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
-<path fill="none" stroke="#d88d56" 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"/>
+<path fill="none" stroke="#5692d8" 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>
</g>
@@ -31,7 +31,7 @@
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
-<path fill="none" stroke="#56c9d8" 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"/>
+<path fill="none" stroke="#d85656" 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>
</g>
@@ -44,7 +44,7 @@
<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M922,-180C922,-180 759,-180 759,-180 753,-180 747,-174 747,-168 747,-168 747,-156 747,-156 747,-150 753,-144 759,-144 759,-144 922,-144 922,-144 928,-144 934,-150 934,-156 934,-156 934,-168 934,-168 934,-174 928,-180 922,-180"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M922,-180C922,-180 759,-180 759,-180 753,-180 747,-174 747,-168 747,-168 747,-156 747,-156 747,-150 753,-144 759,-144 759,-144 922,-144 922,-144 928,-144 934,-150 934,-156 934,-156 934,-168 934,-168 934,-174 928,-180 922,-180"/>
<text text-anchor="middle" x="840.5" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 3->0 -->
@@ -56,7 +56,7 @@
<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
-<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1414.5,-180C1414.5,-180 1268.5,-180 1268.5,-180 1262.5,-180 1256.5,-174 1256.5,-168 1256.5,-168 1256.5,-156 1256.5,-156 1256.5,-150 1262.5,-144 1268.5,-144 1268.5,-144 1414.5,-144 1414.5,-144 1420.5,-144 1426.5,-150 1426.5,-156 1426.5,-156 1426.5,-168 1426.5,-168 1426.5,-174 1420.5,-180 1414.5,-180"/>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M1414.5,-180C1414.5,-180 1268.5,-180 1268.5,-180 1262.5,-180 1256.5,-174 1256.5,-168 1256.5,-168 1256.5,-156 1256.5,-156 1256.5,-150 1262.5,-144 1268.5,-144 1268.5,-144 1414.5,-144 1414.5,-144 1420.5,-144 1426.5,-150 1426.5,-156 1426.5,-156 1426.5,-168 1426.5,-168 1426.5,-174 1420.5,-180 1414.5,-180"/>
<text text-anchor="middle" x="1341.5" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 4->0 -->
@@ -68,7 +68,7 @@
<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1487,-324C1487,-324 1392,-324 1392,-324 1386,-324 1380,-318 1380,-312 1380,-312 1380,-300 1380,-300 1380,-294 1386,-288 1392,-288 1392,-288 1487,-288 1487,-288 1493,-288 1499,-294 1499,-300 1499,-300 1499,-312 1499,-312 1499,-318 1493,-324 1487,-324"/>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1487,-324C1487,-324 1392,-324 1392,-324 1386,-324 1380,-318 1380,-312 1380,-312 1380,-300 1380,-300 1380,-294 1386,-288 1392,-288 1392,-288 1487,-288 1487,-288 1493,-288 1499,-294 1499,-300 1499,-300 1499,-312 1499,-312 1499,-318 1493,-324 1487,-324"/>
<text text-anchor="middle" x="1439.5" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 5->0 -->
@@ -80,7 +80,7 @@
<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1766,-324C1766,-324 1671,-324 1671,-324 1665,-324 1659,-318 1659,-312 1659,-312 1659,-300 1659,-300 1659,-294 1665,-288 1671,-288 1671,-288 1766,-288 1766,-288 1772,-288 1778,-294 1778,-300 1778,-300 1778,-312 1778,-312 1778,-318 1772,-324 1766,-324"/>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1766,-324C1766,-324 1671,-324 1671,-324 1665,-324 1659,-318 1659,-312 1659,-312 1659,-300 1659,-300 1659,-294 1665,-288 1671,-288 1671,-288 1766,-288 1766,-288 1772,-288 1778,-294 1778,-300 1778,-300 1778,-312 1778,-312 1778,-318 1772,-324 1766,-324"/>
<text text-anchor="middle" x="1718.5" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 6->0 -->
@@ -92,7 +92,7 @@
<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M1440.5,-108C1440.5,-108 1312.5,-108 1312.5,-108 1306.5,-108 1300.5,-102 1300.5,-96 1300.5,-96 1300.5,-84 1300.5,-84 1300.5,-78 1306.5,-72 1312.5,-72 1312.5,-72 1440.5,-72 1440.5,-72 1446.5,-72 1452.5,-78 1452.5,-84 1452.5,-84 1452.5,-96 1452.5,-96 1452.5,-102 1446.5,-108 1440.5,-108"/>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1440.5,-108C1440.5,-108 1312.5,-108 1312.5,-108 1306.5,-108 1300.5,-102 1300.5,-96 1300.5,-96 1300.5,-84 1300.5,-84 1300.5,-78 1306.5,-72 1312.5,-72 1312.5,-72 1440.5,-72 1440.5,-72 1446.5,-72 1452.5,-78 1452.5,-84 1452.5,-84 1452.5,-96 1452.5,-96 1452.5,-102 1446.5,-108 1440.5,-108"/>
<text text-anchor="middle" x="1376.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="1376.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
@@ -105,7 +105,7 @@
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M886,-108C886,-108 749,-108 749,-108 743,-108 737,-102 737,-96 737,-96 737,-84 737,-84 737,-78 743,-72 749,-72 749,-72 886,-72 886,-72 892,-72 898,-78 898,-84 898,-84 898,-96 898,-96 898,-102 892,-108 886,-108"/>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M886,-108C886,-108 749,-108 749,-108 743,-108 737,-102 737,-96 737,-96 737,-84 737,-84 737,-78 743,-72 749,-72 749,-72 886,-72 886,-72 892,-72 898,-78 898,-84 898,-84 898,-96 898,-96 898,-102 892,-108 886,-108"/>
<text text-anchor="middle" x="817.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="817.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
@@ -118,7 +118,7 @@
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1078.5,-108C1078.5,-108 928.5,-108 928.5,-108 922.5,-108 916.5,-102 916.5,-96 916.5,-96 916.5,-84 916.5,-84 916.5,-78 922.5,-72 928.5,-72 928.5,-72 1078.5,-72 1078.5,-72 1084.5,-72 1090.5,-78 1090.5,-84 1090.5,-84 1090.5,-96 1090.5,-96 1090.5,-102 1084.5,-108 1078.5,-108"/>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1078.5,-108C1078.5,-108 928.5,-108 928.5,-108 922.5,-108 916.5,-102 916.5,-96 916.5,-96 916.5,-84 916.5,-84 916.5,-78 922.5,-72 928.5,-72 928.5,-72 1078.5,-72 1078.5,-72 1084.5,-72 1090.5,-78 1090.5,-84 1090.5,-84 1090.5,-96 1090.5,-96 1090.5,-102 1084.5,-108 1078.5,-108"/>
<text text-anchor="middle" x="1003.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="1003.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
@@ -131,7 +131,7 @@
<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1270.5,-108C1270.5,-108 1120.5,-108 1120.5,-108 1114.5,-108 1108.5,-102 1108.5,-96 1108.5,-96 1108.5,-84 1108.5,-84 1108.5,-78 1114.5,-72 1120.5,-72 1120.5,-72 1270.5,-72 1270.5,-72 1276.5,-72 1282.5,-78 1282.5,-84 1282.5,-84 1282.5,-96 1282.5,-96 1282.5,-102 1276.5,-108 1270.5,-108"/>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1270.5,-108C1270.5,-108 1120.5,-108 1120.5,-108 1114.5,-108 1108.5,-102 1108.5,-96 1108.5,-96 1108.5,-84 1108.5,-84 1108.5,-78 1114.5,-72 1120.5,-72 1120.5,-72 1270.5,-72 1270.5,-72 1276.5,-72 1282.5,-78 1282.5,-84 1282.5,-84 1282.5,-96 1282.5,-96 1282.5,-102 1276.5,-108 1270.5,-108"/>
<text text-anchor="middle" x="1195.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="1195.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
@@ -144,7 +144,7 @@
<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1574.5,-324C1574.5,-324 1538.5,-324 1538.5,-324 1532.5,-324 1526.5,-318 1526.5,-312 1526.5,-312 1526.5,-300 1526.5,-300 1526.5,-294 1532.5,-288 1538.5,-288 1538.5,-288 1574.5,-288 1574.5,-288 1580.5,-288 1586.5,-294 1586.5,-300 1586.5,-300 1586.5,-312 1586.5,-312 1586.5,-318 1580.5,-324 1574.5,-324"/>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1574.5,-324C1574.5,-324 1538.5,-324 1538.5,-324 1532.5,-324 1526.5,-318 1526.5,-312 1526.5,-312 1526.5,-300 1526.5,-300 1526.5,-294 1532.5,-288 1538.5,-288 1538.5,-288 1574.5,-288 1574.5,-288 1580.5,-288 1586.5,-294 1586.5,-300 1586.5,-300 1586.5,-312 1586.5,-312 1586.5,-318 1580.5,-324 1574.5,-324"/>
<text text-anchor="middle" x="1556.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 11->0 -->
@@ -156,7 +156,7 @@
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
-<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"/>
+<path fill="none" stroke="#d88d56" 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>
</g>
<!-- 11->26 -->
@@ -168,7 +168,7 @@
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<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"/>
+<path fill="none" stroke="#61d856" 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>
</g>
<!-- 12->0 -->
@@ -180,7 +180,7 @@
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<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"/>
+<path fill="none" stroke="#d88d56" 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 -->
@@ -192,7 +192,7 @@
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<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"/>
+<path fill="none" stroke="#56a2d8" 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 -->
@@ -204,7 +204,7 @@
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<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"/>
+<path fill="none" stroke="#56d8d0" 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 -->
@@ -216,7 +216,7 @@
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<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"/>
+<path fill="none" stroke="#56a2d8" 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 -->
@@ -240,7 +240,7 @@
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<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"/>
+<path fill="none" stroke="#56d8a9" 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 -->
@@ -252,7 +252,7 @@
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<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"/>
+<path fill="none" stroke="#56b9d8" 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>
</g>
<!-- 16->19 -->
@@ -264,7 +264,7 @@
<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
-<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"/>
+<path fill="none" stroke="#d86656" 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>
</g>
<!-- 16->24 -->
@@ -276,7 +276,7 @@
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<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"/>
+<path fill="none" stroke="#56d8c1" 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>
</g>
<!-- 17->3 -->
@@ -294,7 +294,7 @@
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<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"/>
+<path fill="none" stroke="#d87d56" 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>
</g>
<!-- 18->4 -->
@@ -306,7 +306,7 @@
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<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"/>
+<path fill="none" stroke="#56d863" 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 -->
@@ -318,7 +318,7 @@
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
-<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"/>
+<path fill="none" stroke="#97d856" 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 -->
@@ -342,7 +342,7 @@
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<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"/>
+<path fill="none" stroke="#d8a456" 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>
@@ -367,7 +367,7 @@
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<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"/>
+<path fill="none" stroke="#d6d856" 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 -->
@@ -397,7 +397,7 @@
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<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"/>
+<path fill="none" stroke="#d8a456" 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>
@@ -476,7 +476,7 @@
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M1928.5,-252C1928.5,-252 1836.5,-252 1836.5,-252 1830.5,-252 1824.5,-246 1824.5,-240 1824.5,-240 1824.5,-228 1824.5,-228 1824.5,-222 1830.5,-216 1836.5,-216 1836.5,-216 1928.5,-216 1928.5,-216 1934.5,-216 1940.5,-222 1940.5,-228 1940.5,-228 1940.5,-240 1940.5,-240 1940.5,-246 1934.5,-252 1928.5,-252"/>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1928.5,-252C1928.5,-252 1836.5,-252 1836.5,-252 1830.5,-252 1824.5,-246 1824.5,-240 1824.5,-240 1824.5,-228 1824.5,-228 1824.5,-222 1830.5,-216 1836.5,-216 1836.5,-216 1928.5,-216 1928.5,-216 1934.5,-216 1940.5,-222 1940.5,-228 1940.5,-228 1940.5,-240 1940.5,-240 1940.5,-246 1934.5,-252 1928.5,-252"/>
<text text-anchor="middle" x="1882.5" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
<!-- 27->13 -->
@@ -500,7 +500,7 @@
<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
-<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"/>
+<path fill="none" stroke="#70d856" 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>
@@ -513,7 +513,7 @@
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M1128,-324C1128,-324 1013,-324 1013,-324 1007,-324 1001,-318 1001,-312 1001,-312 1001,-300 1001,-300 1001,-294 1007,-288 1013,-288 1013,-288 1128,-288 1128,-288 1134,-288 1140,-294 1140,-300 1140,-300 1140,-312 1140,-312 1140,-318 1134,-324 1128,-324"/>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M1128,-324C1128,-324 1013,-324 1013,-324 1007,-324 1001,-318 1001,-312 1001,-312 1001,-300 1001,-300 1001,-294 1007,-288 1013,-288 1013,-288 1128,-288 1128,-288 1134,-288 1140,-294 1140,-300 1140,-300 1140,-312 1140,-312 1140,-318 1134,-324 1128,-324"/>
<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>
@@ -526,7 +526,7 @@
<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
-<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"/>
+<path fill="none" stroke="#bed856" 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>
</g>
@@ -539,7 +539,7 @@
<!-- 31 -->
<g id="node32" class="node">
<title>31</title>
-<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"/>
+<path fill="none" stroke="#56d89a" 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>
</g>
@@ -552,7 +552,7 @@
<!-- 32 -->
<g id="node33" class="node">
<title>32</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1893,-545C1893,-545 1778,-545 1778,-545 1772,-545 1766,-539 1766,-533 1766,-533 1766,-516 1766,-516 1766,-510 1772,-504 1778,-504 1778,-504 1893,-504 1893,-504 1899,-504 1905,-510 1905,-516 1905,-516 1905,-533 1905,-533 1905,-539 1899,-545 1893,-545"/>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1893,-545C1893,-545 1778,-545 1778,-545 1772,-545 1766,-539 1766,-533 1766,-533 1766,-516 1766,-516 1766,-510 1772,-504 1778,-504 1778,-504 1893,-504 1893,-504 1899,-504 1905,-510 1905,-516 1905,-516 1905,-533 1905,-533 1905,-539 1899,-545 1893,-545"/>
<text text-anchor="middle" x="1835.5" y="-533" font-family="sans" font-size="10.00">create_index_star</text>
<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>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 356a382..b57eb38 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -12,17 +12,17 @@
<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M506,-36C506,-36 476,-36 476,-36 470,-36 464,-30 464,-24 464,-24 464,-12 464,-12 464,-6 470,0 476,0 476,0 506,0 506,0 512,0 518,-6 518,-12 518,-12 518,-24 518,-24 518,-30 512,-36 506,-36"/>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M506,-36C506,-36 476,-36 476,-36 470,-36 464,-30 464,-24 464,-24 464,-12 464,-12 464,-6 470,0 476,0 476,0 506,0 506,0 512,0 518,-6 518,-12 518,-12 518,-24 518,-24 518,-30 512,-36 506,-36"/>
<text text-anchor="middle" x="491" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M188,-108C188,-108 148,-108 148,-108 142,-108 136,-102 136,-96 136,-96 136,-84 136,-84 136,-78 142,-72 148,-72 148,-72 188,-72 188,-72 194,-72 200,-78 200,-84 200,-84 200,-96 200,-96 200,-102 194,-108 188,-108"/>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M188,-108C188,-108 148,-108 148,-108 142,-108 136,-102 136,-96 136,-96 136,-84 136,-84 136,-78 142,-72 148,-72 148,-72 188,-72 188,-72 194,-72 200,-78 200,-84 200,-84 200,-96 200,-96 200,-102 194,-108 188,-108"/>
<text text-anchor="middle" x="168" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge1" class="edge">
+<g id="edge4" class="edge">
<title>1->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M200,-74.99C203.01,-73.9 206.05,-72.88 209,-72 294.71,-46.48 398.9,-30.69 453.49,-23.53"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="454.26,-26.96 463.73,-22.21 453.36,-20.02 454.26,-26.96"/>
@@ -30,11 +30,11 @@
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
-<path fill="none" stroke="#56b9d8" stroke-width="2" d="M260,-108C260,-108 230,-108 230,-108 224,-108 218,-102 218,-96 218,-96 218,-84 218,-84 218,-78 224,-72 230,-72 230,-72 260,-72 260,-72 266,-72 272,-78 272,-84 272,-84 272,-96 272,-96 272,-102 266,-108 260,-108"/>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M260,-108C260,-108 230,-108 230,-108 224,-108 218,-102 218,-96 218,-96 218,-84 218,-84 218,-78 224,-72 230,-72 230,-72 260,-72 260,-72 266,-72 272,-78 272,-84 272,-84 272,-96 272,-96 272,-102 266,-108 260,-108"/>
<text text-anchor="middle" x="245" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 2->0 -->
-<g id="edge3" class="edge">
+<g id="edge2" class="edge">
<title>2->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M272.15,-77.12C276.73,-75.3 281.47,-73.52 286,-72 343.68,-52.69 412.45,-36.2 453.87,-26.95"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="454.78,-30.33 463.79,-24.76 453.27,-23.5 454.78,-30.33"/>
@@ -42,11 +42,11 @@
<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M471.5,-468C471.5,-468 308.5,-468 308.5,-468 302.5,-468 296.5,-462 296.5,-456 296.5,-456 296.5,-444 296.5,-444 296.5,-438 302.5,-432 308.5,-432 308.5,-432 471.5,-432 471.5,-432 477.5,-432 483.5,-438 483.5,-444 483.5,-444 483.5,-456 483.5,-456 483.5,-462 477.5,-468 471.5,-468"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M471.5,-468C471.5,-468 308.5,-468 308.5,-468 302.5,-468 296.5,-462 296.5,-456 296.5,-456 296.5,-444 296.5,-444 296.5,-438 302.5,-432 308.5,-432 308.5,-432 471.5,-432 471.5,-432 477.5,-432 483.5,-438 483.5,-444 483.5,-444 483.5,-456 483.5,-456 483.5,-462 477.5,-468 471.5,-468"/>
<text text-anchor="middle" x="390" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 3->0 -->
-<g id="edge8" class="edge">
+<g id="edge6" class="edge">
<title>3->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M450.25,-431.97C470.89,-423.78 492.82,-412.12 509,-396 539.72,-365.39 549,-350.37 549,-307 549,-307 549,-307 549,-161 549,-117.7 525.6,-72.11 508.52,-44.61"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="511.36,-42.55 503.02,-36.01 505.46,-46.32 511.36,-42.55"/>
@@ -54,11 +54,11 @@
<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M660,-468C660,-468 514,-468 514,-468 508,-468 502,-462 502,-456 502,-456 502,-444 502,-444 502,-438 508,-432 514,-432 514,-432 660,-432 660,-432 666,-432 672,-438 672,-444 672,-444 672,-456 672,-456 672,-462 666,-468 660,-468"/>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M660,-468C660,-468 514,-468 514,-468 508,-468 502,-462 502,-456 502,-456 502,-444 502,-444 502,-438 508,-432 514,-432 514,-432 660,-432 660,-432 666,-432 672,-438 672,-444 672,-444 672,-456 672,-456 672,-462 666,-468 660,-468"/>
<text text-anchor="middle" x="587" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 4->0 -->
-<g id="edge10" class="edge">
+<g id="edge8" class="edge">
<title>4->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M587,-431.95C587,-405.29 587,-352.11 587,-307 587,-307 587,-307 587,-161 587,-120.03 586.13,-105.82 563,-72 553.82,-58.57 540.08,-47.25 527.07,-38.57"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="528.56,-35.37 518.23,-32.99 524.82,-41.29 528.56,-35.37"/>
@@ -66,11 +66,11 @@
<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M450.5,-324C450.5,-324 355.5,-324 355.5,-324 349.5,-324 343.5,-318 343.5,-312 343.5,-312 343.5,-300 343.5,-300 343.5,-294 349.5,-288 355.5,-288 355.5,-288 450.5,-288 450.5,-288 456.5,-288 462.5,-294 462.5,-300 462.5,-300 462.5,-312 462.5,-312 462.5,-318 456.5,-324 450.5,-324"/>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M450.5,-324C450.5,-324 355.5,-324 355.5,-324 349.5,-324 343.5,-318 343.5,-312 343.5,-312 343.5,-300 343.5,-300 343.5,-294 349.5,-288 355.5,-288 355.5,-288 450.5,-288 450.5,-288 456.5,-288 462.5,-294 462.5,-300 462.5,-300 462.5,-312 462.5,-312 462.5,-318 456.5,-324 450.5,-324"/>
<text text-anchor="middle" x="403" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 5->0 -->
-<g id="edge6" class="edge">
+<g id="edge7" class="edge">
<title>5->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M446.39,-287.77C461.66,-279.38 477.21,-267.65 486,-252 523.15,-185.9 508.59,-91.71 498.12,-45.99"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="501.51,-45.12 495.77,-36.22 494.7,-46.76 501.51,-45.12"/>
@@ -78,11 +78,11 @@
<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M775,-396C775,-396 647,-396 647,-396 641,-396 635,-390 635,-384 635,-384 635,-372 635,-372 635,-366 641,-360 647,-360 647,-360 775,-360 775,-360 781,-360 787,-366 787,-372 787,-372 787,-384 787,-384 787,-390 781,-396 775,-396"/>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M775,-396C775,-396 647,-396 647,-396 641,-396 635,-390 635,-384 635,-384 635,-372 635,-372 635,-366 641,-360 647,-360 647,-360 775,-360 775,-360 781,-360 787,-366 787,-372 787,-372 787,-384 787,-384 787,-390 781,-396 775,-396"/>
<text text-anchor="middle" x="711" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 6->0 -->
-<g id="edge2" class="edge">
+<g id="edge5" class="edge">
<title>6->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M700.02,-359.84C684.49,-333.89 658,-282.63 658,-235 658,-235 658,-235 658,-161 658,-93.03 576.72,-50.79 527.57,-31.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="528.79,-28.17 518.2,-27.89 526.31,-34.72 528.79,-28.17"/>
@@ -90,11 +90,11 @@
<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M967,-396C967,-396 817,-396 817,-396 811,-396 805,-390 805,-384 805,-384 805,-372 805,-372 805,-366 811,-360 817,-360 817,-360 967,-360 967,-360 973,-360 979,-366 979,-372 979,-372 979,-384 979,-384 979,-390 973,-396 967,-396"/>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M967,-396C967,-396 817,-396 817,-396 811,-396 805,-390 805,-384 805,-384 805,-372 805,-372 805,-366 811,-360 817,-360 817,-360 967,-360 967,-360 973,-360 979,-366 979,-372 979,-372 979,-384 979,-384 979,-390 973,-396 967,-396"/>
<text text-anchor="middle" x="892" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 7->0 -->
-<g id="edge9" class="edge">
+<g id="edge3" class="edge">
<title>7->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M871.12,-359.63C843.98,-334.97 800,-286.99 800,-235 800,-235 800,-235 800,-161 800,-42.65 610.53,-22.58 528.32,-19.44"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="528.26,-15.94 518.15,-19.12 528.04,-22.93 528.26,-15.94"/>
@@ -102,11 +102,11 @@
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M313,-324C313,-324 277,-324 277,-324 271,-324 265,-318 265,-312 265,-312 265,-300 265,-300 265,-294 271,-288 277,-288 277,-288 313,-288 313,-288 319,-288 325,-294 325,-300 325,-300 325,-312 325,-312 325,-318 319,-324 313,-324"/>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M313,-324C313,-324 277,-324 277,-324 271,-324 265,-318 265,-312 265,-312 265,-300 265,-300 265,-294 271,-288 277,-288 277,-288 313,-288 313,-288 319,-288 325,-294 325,-300 325,-300 325,-312 325,-312 325,-318 319,-324 313,-324"/>
<text text-anchor="middle" x="295" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 8->0 -->
-<g id="edge4" class="edge">
+<g id="edge1" class="edge">
<title>8->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M325.02,-290.82C342.15,-281.6 363.11,-268.27 378,-252 435.3,-189.42 469.53,-92.48 483.56,-45.85"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="486.94,-46.75 486.4,-36.17 480.23,-44.78 486.94,-46.75"/>
@@ -114,7 +114,7 @@
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M357,-252C357,-252 235,-252 235,-252 229,-252 223,-246 223,-240 223,-240 223,-228 223,-228 223,-222 229,-216 235,-216 235,-216 357,-216 357,-216 363,-216 369,-222 369,-228 369,-228 369,-240 369,-240 369,-246 363,-252 357,-252"/>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M357,-252C357,-252 235,-252 235,-252 229,-252 223,-246 223,-240 223,-240 223,-228 223,-228 223,-222 229,-216 235,-216 235,-216 357,-216 357,-216 363,-216 369,-222 369,-228 369,-228 369,-240 369,-240 369,-246 363,-252 357,-252"/>
<text text-anchor="middle" x="296" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
<!-- 8->20 -->
@@ -126,11 +126,11 @@
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M314,-180C314,-180 284,-180 284,-180 278,-180 272,-174 272,-168 272,-168 272,-156 272,-156 272,-150 278,-144 284,-144 284,-144 314,-144 314,-144 320,-144 326,-150 326,-156 326,-156 326,-168 326,-168 326,-174 320,-180 314,-180"/>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M314,-180C314,-180 284,-180 284,-180 278,-180 272,-174 272,-168 272,-168 272,-156 272,-156 272,-150 278,-144 284,-144 284,-144 314,-144 314,-144 320,-144 326,-150 326,-156 326,-156 326,-168 326,-168 326,-174 320,-180 314,-180"/>
<text text-anchor="middle" x="299" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 9->0 -->
-<g id="edge7" class="edge">
+<g id="edge9" class="edge">
<title>9->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M298.06,-143.96C297.93,-124.14 300.83,-91.65 319,-72 353.79,-34.39 414.57,-23.22 453.78,-20.04"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="454.24,-23.52 463.99,-19.36 453.77,-16.53 454.24,-23.52"/>
@@ -138,7 +138,7 @@
<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M432,-108C432,-108 340,-108 340,-108 334,-108 328,-102 328,-96 328,-96 328,-84 328,-84 328,-78 334,-72 340,-72 340,-72 432,-72 432,-72 438,-72 444,-78 444,-84 444,-84 444,-96 444,-96 444,-102 438,-108 432,-108"/>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M432,-108C432,-108 340,-108 340,-108 334,-108 328,-102 328,-96 328,-96 328,-84 328,-84 328,-78 334,-72 340,-72 340,-72 432,-72 432,-72 438,-72 444,-78 444,-84 444,-84 444,-96 444,-96 444,-102 438,-108 432,-108"/>
<text text-anchor="middle" x="386" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 9->10 -->
@@ -148,7 +148,7 @@
<polygon fill="grey" stroke="grey" stroke-width="2" points="359.14,-117.1 364.74,-108.1 354.76,-111.65 359.14,-117.1"/>
</g>
<!-- 10->0 -->
-<g id="edge5" class="edge">
+<g id="edge10" class="edge">
<title>10->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M411.69,-71.88C425.29,-62.81 442.17,-51.55 456.86,-41.76"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="458.84,-44.65 465.22,-36.19 454.95,-38.82 458.84,-44.65"/>
@@ -156,7 +156,7 @@
<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M413,-540C413,-540 285,-540 285,-540 279,-540 273,-534 273,-528 273,-528 273,-516 273,-516 273,-510 279,-504 285,-504 285,-504 413,-504 413,-504 419,-504 425,-510 425,-516 425,-516 425,-528 425,-528 425,-534 419,-540 413,-540"/>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M413,-540C413,-540 285,-540 285,-540 279,-540 273,-534 273,-528 273,-528 273,-516 273,-516 273,-510 279,-504 285,-504 285,-504 413,-504 413,-504 419,-504 425,-510 425,-516 425,-516 425,-528 425,-528 425,-534 419,-540 413,-540"/>
<text text-anchor="middle" x="349" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 11->3 -->
@@ -168,11 +168,11 @@
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<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"/>
+<path fill="none" stroke="#56b9d8" 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="edge32" class="edge">
+<g id="edge33" class="edge">
<title>11->14</title>
<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"/>
@@ -180,11 +180,11 @@
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<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"/>
+<path fill="none" stroke="#56c9d8" 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">
+<g id="edge38" class="edge">
<title>11->18</title>
<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"/>
@@ -192,7 +192,7 @@
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<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"/>
+<path fill="none" stroke="#70d856" 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 -->
@@ -202,7 +202,7 @@
<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">
+<g id="edge13" class="edge">
<title>12->4</title>
<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"/>
@@ -210,11 +210,11 @@
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<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"/>
+<path fill="none" stroke="#56a2d8" 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">
+<g id="edge14" class="edge">
<title>13->4</title>
<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"/>
@@ -222,11 +222,11 @@
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<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"/>
+<path fill="none" stroke="#56d873" 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="edge36" class="edge">
+<g id="edge37" class="edge">
<title>13->17</title>
<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"/>
@@ -234,17 +234,17 @@
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<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"/>
+<path fill="none" stroke="#d85656" 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="edge40" class="edge">
+<g id="edge41" class="edge">
<title>13->19</title>
<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="edge18" class="edge">
+<g id="edge17" class="edge">
<title>14->5</title>
<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"/>
@@ -258,7 +258,7 @@
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<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"/>
+<path fill="none" stroke="#56d8c1" 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 -->
@@ -268,13 +268,13 @@
<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">
+<g id="edge15" class="edge">
<title>15->5</title>
<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">
+<g id="edge23" class="edge">
<title>15->8</title>
<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"/>
@@ -282,23 +282,23 @@
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<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"/>
+<path fill="none" stroke="#88d856" 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="edge17" class="edge">
+<g id="edge18" class="edge">
<title>16->5</title>
<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="edge15" class="edge">
+<g id="edge16" class="edge">
<title>17->5</title>
<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="edge23" class="edge">
+<g id="edge24" class="edge">
<title>17->8</title>
<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"/>
@@ -342,7 +342,7 @@
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M104,-252C104,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 104,-216 104,-216 110,-216 116,-222 116,-228 116,-228 116,-240 116,-240 116,-246 110,-252 104,-252"/>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M104,-252C104,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 104,-216 104,-216 110,-216 116,-222 116,-228 116,-228 116,-240 116,-240 116,-246 110,-252 104,-252"/>
<text text-anchor="middle" x="58" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
<!-- 21->9 -->
@@ -354,7 +354,7 @@
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M416.5,-612C416.5,-612 273.5,-612 273.5,-612 267.5,-612 261.5,-606 261.5,-600 261.5,-600 261.5,-588 261.5,-588 261.5,-582 267.5,-576 273.5,-576 273.5,-576 416.5,-576 416.5,-576 422.5,-576 428.5,-582 428.5,-588 428.5,-588 428.5,-600 428.5,-600 428.5,-606 422.5,-612 416.5,-612"/>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M416.5,-612C416.5,-612 273.5,-612 273.5,-612 267.5,-612 261.5,-606 261.5,-600 261.5,-600 261.5,-588 261.5,-588 261.5,-582 267.5,-576 273.5,-576 273.5,-576 416.5,-576 416.5,-576 422.5,-576 428.5,-582 428.5,-588 428.5,-588 428.5,-600 428.5,-600 428.5,-606 422.5,-612 416.5,-612"/>
<text text-anchor="middle" x="345" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 22->11 -->
@@ -366,7 +366,7 @@
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<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"/>
+<path fill="none" stroke="#61d856" 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"/>
<text text-anchor="middle" x="733" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 23->12 -->
@@ -378,7 +378,7 @@
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
-<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"/>
+<path fill="none" stroke="#567bd8" 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"/>
<text text-anchor="middle" x="802" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 23->26 -->
@@ -390,7 +390,7 @@
<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M584,-612C584,-612 458,-612 458,-612 452,-612 446,-606 446,-600 446,-600 446,-588 446,-588 446,-582 452,-576 458,-576 458,-576 584,-576 584,-576 590,-576 596,-582 596,-588 596,-588 596,-600 596,-600 596,-606 590,-612 584,-612"/>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M584,-612C584,-612 458,-612 458,-612 452,-612 446,-606 446,-600 446,-600 446,-588 446,-588 446,-582 452,-576 458,-576 458,-576 584,-576 584,-576 590,-576 596,-582 596,-588 596,-588 596,-600 596,-600 596,-606 590,-612 584,-612"/>
<text text-anchor="middle" x="521" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 24->13 -->
@@ -402,17 +402,17 @@
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M131,-540C131,-540 51,-540 51,-540 45,-540 39,-534 39,-528 39,-528 39,-516 39,-516 39,-510 45,-504 51,-504 51,-504 131,-504 131,-504 137,-504 143,-510 143,-516 143,-516 143,-528 143,-528 143,-534 137,-540 131,-540"/>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M131,-540C131,-540 51,-540 51,-540 45,-540 39,-534 39,-528 39,-528 39,-516 39,-516 39,-510 45,-504 51,-504 51,-504 131,-504 131,-504 137,-504 143,-510 143,-516 143,-516 143,-528 143,-528 143,-534 137,-540 131,-540"/>
<text text-anchor="middle" x="91" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 25->14 -->
-<g id="edge33" class="edge">
+<g id="edge32" class="edge">
<title>25->14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M91,-503.7C91,-495.98 91,-486.71 91,-478.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="94.5,-478.1 91,-468.1 87.5,-478.1 94.5,-478.1"/>
</g>
<!-- 25->17 -->
-<g id="edge37" class="edge">
+<g id="edge36" class="edge">
<title>25->17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M123.78,-503.88C141.63,-494.55 163.9,-482.92 183,-472.94"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="184.85,-475.92 192.09,-468.19 181.61,-469.72 184.85,-475.92"/>
@@ -424,13 +424,13 @@
<polygon fill="grey" stroke="grey" stroke-width="2" points="46.65,-262.52 48.2,-252.04 40.45,-259.26 46.65,-262.52"/>
</g>
<!-- 26->18 -->
-<g id="edge38" class="edge">
+<g id="edge39" class="edge">
<title>26->18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M791.87,-503.7C787.15,-495.64 781.44,-485.89 776.22,-476.98"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="779.09,-474.96 771.02,-468.1 773.05,-478.5 779.09,-474.96"/>
</g>
<!-- 26->19 -->
-<g id="edge41" class="edge">
+<g id="edge40" class="edge">
<title>26->19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M829.15,-503.88C843.53,-494.81 861.38,-483.55 876.91,-473.76"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="879.15,-476.48 885.74,-468.19 875.42,-470.56 879.15,-476.48"/>
diff --git a/tests/test_alfa/expected_output.md5 b/tests/test_alfa/expected_output.md5
index 0d85572..57f9dfd 100644
--- a/tests/test_alfa/expected_output.md5
+++ b/tests/test_alfa/expected_output.md5
@@ -1,16 +1,30 @@
-6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
-2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
-0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg
-c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg
-0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg
-c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str2.out.bg
-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
-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
-ea91b4f85622561158bff2f7c9c312b3 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.UniqueMultiple.str1.out.bg
-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.UniqueMultiple.str2.out.bg
-ea91b4f85622561158bff2f7c9c312b3 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.str1.out.bg
-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
-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
-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
+90e42aa46890e9cd0a47800428699fbf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
+ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.Unique.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.Unique.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.Unique.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.Unique.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.plus.bg
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
diff --git a/tests/test_alfa/input_files/config.yaml b/tests/test_alfa/input_files/config.yaml
new file mode 100644
index 0000000..0304e06
--- /dev/null
+++ b/tests/test_alfa/input_files/config.yaml
@@ -0,0 +1,9 @@
+---
+ samples: "input_files/samples.tsv"
+ output_dir: "results/"
+ log_dir: "logs/"
+ kallisto_indexes: "results/kallisto_indexes/"
+ salmon_indexes: "results/salmon_indexes/"
+ star_indexes: "results/star_indexes/"
+ alfa_indexes: "results/alfa_indexes/"
+...
diff --git a/tests/test_alfa/input_files/homo_sapiens/quick_start.gtf b/tests/test_alfa/input_files/homo_sapiens/quick_start.gtf
new file mode 100644
index 0000000..4e9c0b9
--- /dev/null
+++ b/tests/test_alfa/input_files/homo_sapiens/quick_start.gtf
@@ -0,0 +1,6 @@
+Chr1 ensembl_havana gene 251 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana transcript 251 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana exon 376 1000 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana CDS 376 1000 . + 0 gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana five_prime_utr 251 375 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana three_prime_utr 1001 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
diff --git a/tests/test_alfa/input_files/samples.tsv b/tests/test_alfa/input_files/samples.tsv
new file mode 100644
index 0000000..66ab290
--- /dev/null
+++ b/tests/test_alfa/input_files/samples.tsv
@@ -0,0 +1,5 @@
+sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya
+paired_end_R1_on_plus_sense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX GATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens input_files/homo_sapiens/quick_start.gtf input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+paired_end_R1_on_plus_antisense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens input_files/homo_sapiens/quick_start.gtf input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+paired_end_R1_on_minus_sense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens input_files/homo_sapiens/quick_start.gtf input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+paired_end_R1_on_minus_antisense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens input_files/homo_sapiens/quick_start.gtf input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam
new file mode 100644
index 0000000000000000000000000000000000000000..5aabbdab18d2fde5d02988776ef0c7083fe7e072
GIT binary patch
literal 767
zcmb2|=3rp}f&Xj_PR>jW&5Ua&-OoB?AaYFmw!~M>PfXwXcNkWsu6@B0Jy$f}JEQL#
z&*YNKU01K)oxEmkj=|hF#~g|t%+Zg3@ICcO``q8shb8R#&-y;udF?=tc%0VKB#jkq
z?+oe;AD`ehdOGWK)P?$jU5B4unbW(s;_dn~sU>S>C;R@ocHq_J7VoxbmNd4{w|os&
z3awDs`l?yr((9E$Ym8Z^xE?9Jb&jv)iGiEzo0yZ~9;J!J0W)qZUX^r;yl&&Zar5<m
zIZv%Tf6H*Og??(Z@?Q4(<i%ZOb05fc&D@b8I%Ss8tZZwSi9GXKw*6+leu-=6)}^g=
z%5PtNO<5_ux}zvU>qe5R)ZOnI-<)etH1_=2kasjFGhwmw2j=(NyV*piRrk($Cb(R*
z&_6ArVAW-vN$(dt>pie>&haqk?>mHz7fuyPEWWrhyj()(%q9lcpp%xOJ#PXV-2D>c
zJCD1HEDwy+Jn{cv%&}kQ8$O>n$NajC=kSiz<)82No{v8KgXxq1f;<Ig1_tyvh+{l^
z>AYXFfeibHMdtZB-Z4o^P7B`}O%Jg0`n_AwCg<b%*5=*S-(|}_zf-O#?%&QHpmqDr
z5sME;%o$I8|Kj;McCnQ(`@+}#M-MpWYizWd{PS_rsr>gA{f(ztx^yOL=}+?x2q@Jo
zP~FO~c5_bKIzK@v-WqcWzS!wIwd+l}{_gqpOut!LpF>GF%jn;!NC%D8{W-tiB%R~`
zd}yXVm%4uU$<MWgoAL@y+ZEr}z4gR?d-PPNrIH@1Q>?E1vfpwr%zNL~t=*E59=Xdi
z`L|s5dTp{bwSVhb&63@>Ri+&<wiTXm%qZ{V)@292J=%MzPWJh<+Gp>!ZTOkGbGBK`
zye6?I=T+KY?nk{pboj<`i%*72b(XZWOktg3=yt~5^7xV6Jp~>fE~~q?T%2ZmZJlnU
xZR>KqTP??BcJ#Hjm`rvmpVuU6miNr!`_}V!{Nuv+MP6dV3|?slW>A6$V*rIVZkYf8
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..95b615abec731d3dfd080ff2d6067edbaa051806
GIT binary patch
literal 96
ycmZ>A^kigYU|?WkU|{eRVqgHV85mk16vJbXFoV}5h&;MD7XvDQXoBg5$N>OI&;@S*
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam
new file mode 100644
index 0000000000000000000000000000000000000000..5aabbdab18d2fde5d02988776ef0c7083fe7e072
GIT binary patch
literal 767
zcmb2|=3rp}f&Xj_PR>jW&5Ua&-OoB?AaYFmw!~M>PfXwXcNkWsu6@B0Jy$f}JEQL#
z&*YNKU01K)oxEmkj=|hF#~g|t%+Zg3@ICcO``q8shb8R#&-y;udF?=tc%0VKB#jkq
z?+oe;AD`ehdOGWK)P?$jU5B4unbW(s;_dn~sU>S>C;R@ocHq_J7VoxbmNd4{w|os&
z3awDs`l?yr((9E$Ym8Z^xE?9Jb&jv)iGiEzo0yZ~9;J!J0W)qZUX^r;yl&&Zar5<m
zIZv%Tf6H*Og??(Z@?Q4(<i%ZOb05fc&D@b8I%Ss8tZZwSi9GXKw*6+leu-=6)}^g=
z%5PtNO<5_ux}zvU>qe5R)ZOnI-<)etH1_=2kasjFGhwmw2j=(NyV*piRrk($Cb(R*
z&_6ArVAW-vN$(dt>pie>&haqk?>mHz7fuyPEWWrhyj()(%q9lcpp%xOJ#PXV-2D>c
zJCD1HEDwy+Jn{cv%&}kQ8$O>n$NajC=kSiz<)82No{v8KgXxq1f;<Ig1_tyvh+{l^
z>AYXFfeibHMdtZB-Z4o^P7B`}O%Jg0`n_AwCg<b%*5=*S-(|}_zf-O#?%&QHpmqDr
z5sME;%o$I8|Kj;McCnQ(`@+}#M-MpWYizWd{PS_rsr>gA{f(ztx^yOL=}+?x2q@Jo
zP~FO~c5_bKIzK@v-WqcWzS!wIwd+l}{_gqpOut!LpF>GF%jn;!NC%D8{W-tiB%R~`
zd}yXVm%4uU$<MWgoAL@y+ZEr}z4gR?d-PPNrIH@1Q>?E1vfpwr%zNL~t=*E59=Xdi
z`L|s5dTp{bwSVhb&63@>Ri+&<wiTXm%qZ{V)@292J=%MzPWJh<+Gp>!ZTOkGbGBK`
zye6?I=T+KY?nk{pboj<`i%*72b(XZWOktg3=yt~5^7xV6Jp~>fE~~q?T%2ZmZJlnU
xZR>KqTP??BcJ#Hjm`rvmpVuU6miNr!`_}V!{Nuv+MP6dV3|?slW>A6$V*rIVZkYf8
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..95b615abec731d3dfd080ff2d6067edbaa051806
GIT binary patch
literal 96
ycmZ>A^kigYU|?WkU|{eRVqgHV85mk16vJbXFoV}5h&;MD7XvDQXoBg5$N>OI&;@S*
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam
new file mode 100644
index 0000000000000000000000000000000000000000..e4b8cb341acae604db9eba2f3eb23d9510ca783c
GIT binary patch
literal 768
zcmb2|=3rp}f&Xj_PR>jW&5Ua&-OoB?AaYFmw!~M>PfXwXcNkWsu6@B0Jy$f}JEQL#
z&*YNKU01K)oxEmkj=|hF#~g|t%+Zg3@ICcO``q8shb8R#&-y;udF?=tc%0VKB#jkq
z?+oe;AD`ehdOGWK)P?$jU5B4unbW(s;_dn~sU>S>C;R@ocHq_J7VoxbmNd4{w|os&
z3awDs`l?yr((9E$Ym8Z^xE?9Jb&jv)iGiEzo0yZ~9;J!J0W)qZUX^r;yl&&Zar5<m
zIZv%Tf6H*Og??(Z@?Q4(<i%ZOb05fc&D@b8I%Ss8tZZwSi9GXKw*6+leu-=6)}^g=
z%5PtNO<5_ux}zvU>qe5R)ZOnI-<)etH1_=2kasjFGhwmw2j=(NyV*piRrk($Cb(R*
z&_6ArVAW-vN$(dt>pie>&haqk?>mHz7fuyPEWWrhyj()(%q9lcpp%xOJ#PXV-2D>c
zJCD1HEDwy+Jn{cv%&}kQ8$O>n$NajC=kSiz<)82No{v8KgXxq1f;<Ig1_tyvh-W-|
z$=2_%fedQ_yV<sosViDsJm%b3=e5)#Pv-Z2*TjsY$1gR$dvj-@bameWxBlzQ4nDUY
z3AxPns|*r)?rR^J-}<UYrX|ll-Ijgtf+MedmYv^hxWE2^4V#{@#wM3ldm?lk9Iq}t
zF!c)4mUEjpcUih;T=;x<!Ts{sXL^61Dt!6;YWDuG@AfEk_^dej!CIVg;TpS5XE*m+
z+WT^+TWQa!iR+1z@7^5R99=f^cj862<#+Nzxu&KmOby72fBpXwo3!rFi`VqhQWUq&
zU3T|!pZ40zSEk8cGh2S)UEbsfrt@E19HdVF@K|Tcx=r}~ly9#Mw!bkd-`)CE{&cMT
z;isAz3r&~oa{9mi>pGjB+8$;3;8RXs9v+bnlF3K@O!oHK^O~c*#bwK?6Na}o9lkYH
zb@lQO_uOWGn8AE~<Ae!mK`*WaZ#dL;R_58c-DmzXwOkDDyTpbWzS0cLpcD_r0AOWx
A@Bjb+
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..f4e7b055bba5939ace1f1baac5ef5c2f99a9edb2
GIT binary patch
literal 96
ycmZ>A^kigYU|?WkU|{eRVqgHV85mk16vGpcFoV}5h&;MD7XvDQXoBg5$N>OJJOyz8
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam
new file mode 100644
index 0000000000000000000000000000000000000000..e4b8cb341acae604db9eba2f3eb23d9510ca783c
GIT binary patch
literal 768
zcmb2|=3rp}f&Xj_PR>jW&5Ua&-OoB?AaYFmw!~M>PfXwXcNkWsu6@B0Jy$f}JEQL#
z&*YNKU01K)oxEmkj=|hF#~g|t%+Zg3@ICcO``q8shb8R#&-y;udF?=tc%0VKB#jkq
z?+oe;AD`ehdOGWK)P?$jU5B4unbW(s;_dn~sU>S>C;R@ocHq_J7VoxbmNd4{w|os&
z3awDs`l?yr((9E$Ym8Z^xE?9Jb&jv)iGiEzo0yZ~9;J!J0W)qZUX^r;yl&&Zar5<m
zIZv%Tf6H*Og??(Z@?Q4(<i%ZOb05fc&D@b8I%Ss8tZZwSi9GXKw*6+leu-=6)}^g=
z%5PtNO<5_ux}zvU>qe5R)ZOnI-<)etH1_=2kasjFGhwmw2j=(NyV*piRrk($Cb(R*
z&_6ArVAW-vN$(dt>pie>&haqk?>mHz7fuyPEWWrhyj()(%q9lcpp%xOJ#PXV-2D>c
zJCD1HEDwy+Jn{cv%&}kQ8$O>n$NajC=kSiz<)82No{v8KgXxq1f;<Ig1_tyvh-W-|
z$=2_%fedQ_yV<sosViDsJm%b3=e5)#Pv-Z2*TjsY$1gR$dvj-@bameWxBlzQ4nDUY
z3AxPns|*r)?rR^J-}<UYrX|ll-Ijgtf+MedmYv^hxWE2^4V#{@#wM3ldm?lk9Iq}t
zF!c)4mUEjpcUih;T=;x<!Ts{sXL^61Dt!6;YWDuG@AfEk_^dej!CIVg;TpS5XE*m+
z+WT^+TWQa!iR+1z@7^5R99=f^cj862<#+Nzxu&KmOby72fBpXwo3!rFi`VqhQWUq&
zU3T|!pZ40zSEk8cGh2S)UEbsfrt@E19HdVF@K|Tcx=r}~ly9#Mw!bkd-`)CE{&cMT
z;isAz3r&~oa{9mi>pGjB+8$;3;8RXs9v+bnlF3K@O!oHK^O~c*#bwK?6Na}o9lkYH
zb@lQO_uOWGn8AE~<Ae!mK`*WaZ#dL;R_58c-DmzXwOkDDyTpbWzS0cLpcD_r0AOWx
A@Bjb+
literal 0
HcmV?d00001
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..f4e7b055bba5939ace1f1baac5ef5c2f99a9edb2
GIT binary patch
literal 96
ycmZ>A^kigYU|?WkU|{eRVqgHV85mk16vGpcFoV}5h&;MD7XvDQXoBg5$N>OJJOyz8
literal 0
HcmV?d00001
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_Aligned.sortedByCoord.out.bam 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_Aligned.sortedByCoord.out.bam
deleted file mode 100644
index 0b04abaa1b83145ed74a8b60d76a06052ca876b8..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 2227
zcmb2|=3rp}f&Xj_PR>jW{!CY=-Os;eAaMNh@ec->{~ParbMeSno@Mhf`?b}?101(k
zKRp`0Vakn_Z?|07U)QJE5x^vTo7q{Z@%O#hbLscpUw%Kd+JD{SlKp&l=Lf2P$h%W<
z$FpU^l)^;|FZS-=y-{#hW4_(lvdU8TV+rpZ7hCTve&0T~;@a$8lQU|~GjH8nTkd=3
z;E5;!r?bm+Dl{|{CT+5u&$KWrd7kc)pVAAZvu7}iOY+Qg5ek`@bv0;~#~F)O)fLyA
zQkb+S89!K6`g>#Ov-s}UC2E(&r#0<*e*4E915Od<<+@uRRWZ&|wfIo@a`lJRQLE<&
zKlVIvMEF6>6744A%f}8>D|p#geHIUXrYd^vp6;4khZ;{99n!4w?6}vl=)zL5i9BjT
zayLH3>#8YR#^wLDd{_}2vqtmPcPAO{m5txRo8LO#tGKcFd-Lq)PaOhPeuQ;aFN}K{
za7_C0K_2UMF4-sRM5RPtEzJzo{&wkotMB`uv^QyaD(YNvh3ASksC~Y%q4?OZ)wdTr
zo_pgI_R&0frPjimx@o7njW)S7)<^URD<*pVkO>I*y20zjj~|>*R_HMPy!SOuXwhWX
zDYD-awKnH1`l9Lm(YBtKfxF}U9If4KpOe+j9QFDY`NT!@^u$eDd*5Aol)k?AU8QeM
z348MP0ENI$Ri93$$fgLE2_)oe-%`JI|HGU83vQ}T-FkSFRgdhv3(AiRvn=!^I!%{Y
z9X)BTv*xp<)k*b<g;Elw7OM~cn6LQF=fJhXm4#0&&RKt6yGOzDy}iY`{A2fCCq{EJ
zFrcR=H@2-a&i37L5oxt$4pI|}$XqQIDbcw4iR-~EtIL<~8n0eC%W0*?ES(c=DU42v
z-7XqjADAvLjjG@mk}lihP{CWahfVs%CaH6Kx7~gjrY3PR#OR-<`owe3i_h;pcQEeI
z>tl|SYKltDZ+pwBf1kB>$&q{4ckKKB;Kzp#8QZL4b^HAO9=`ou?w0lZ`SZ{DrEk9Z
z@XeQRZwgvpA3o~&>C;;kL$mH<)`8cx+>+-6?7ZsaGTmA`TfRtkk?zJzMf-Q<O%08j
zdep>sxoe=$X%pQbnN^DpO)OiU*;v2e!1~Op`}5!b-2J@z*}<Rv=k?D`{{3TTLI1Sl
zCpUBdp7ABtc6avtPe-p_y?WGAE>>m!-O4X_Kd;|c|LN^?{dxN;KApY%+<#K@G}f1S
z5q~x$I@Z)3yZ<j=XO6(JQ!B19BrOWAT$8$DYp~X}xZ8L9zgX>O<z2EwXJOlsrJ0;d
zEs~6NXEHP<s9k4V{q5jp9ryH)udQXf?}_hE%<s^D_Ia`Jr=wl9f>S4C=Qo$l{F0^{
znrbZi(roj_GObwxtUnj2#81)LV!6%yMkDJ9t_H^$3|$Nt&CaoITzqv-*T-7NUFEfo
zHElnV+Fj?Rp7LC3n{wLgcgEJ!TQ_PgD%vwAV&yCEpsg2~vnO~6ERZ^|^WuF21%tP@
zoZ4pBs#)#Qx2xTreDU`q?l-(2j^^x(D2mg$DbDq9K~u=gRW5p|vQA>5zE2mr$QorH
zxwX>UsC?)BuGd@M&GW8`^V>P0fH(Vr(3}%eE995BbLK4GtZ;YtJ_S4GnvI8*QYzOj
z-L|VwQR`*)$|Fa(SC?LJv&vMqh;?GV;>aK3DDBxC#FBP$qeUv$|F*7LL%VK!bDgSq
znI(s7HqM%>Gg17s^EcOZi_WPXn%z0+MBo>p^#!Zemdq3~6E=(gZCqA9S-dwXAtCxf
zsCl|fBj=O@D-%MlcocYBTP&JY(K~<clIrW?N76g=w?#@kp2+R^s71n*LFwaevB1!+
z!jn5o@`M)b2xZD#BEElRZ-JnL)$6%JQ>Tec=f0ck@$lgPDdP6I5nuLISY8nSJo#v$
zeSF6HW}aJB%X!qemTMZ!;S$u_82HrGDD<G%iixkEb8lm7bUfR@^RsE2LFfckGYLk0
z+5K)F-`DAPoEM1C*<7H(!o}0xvf+?LFDJL|)m1+2Q9f%7r*7OH;hJAEgLyLBN!O+Y
z0tWGd?6)coH|aZ+Y<aWi;<>2(`=_hOf4=kcblSCF%+<`lP9&B3<fiO=u!Cb~@6;_4
zDp}D_!!#EzK6++m>sHsCh|X!R@=6OYa=mqJ4%}{`BEh+wB~*at(7Xq2J-lm@N<>t4
zJAO=PZu-Ep;iwsx@KhzCshw`wjaM4{L&7AVA96|Edg<H^?`ux~o@Fw*S2S)7%GppO
zv&_}KRjzdPakHYRl65<N*0nDxZ#{I6A$*NN>;&z;8=|347Z+T7`1!Ew70$E(QG>~s
z*B;-udQWkNk_ICmx5nbeNvz+r7D~@o6cO!Uk2(?R6@98pEmJf5XL?Eagg3F_0`nNx
z-EeC>ZzSTlOmOlo%Z~OUZ;nOZv*&9{X6c_Zb9%Ap>ha5Lc^L<VHn?8A&6Hymb*1p9
z)Vc%nrFdPx$9@aD_%!W(7ykzH1EQO+o_w@{pIbeUyG&?m@r$JgPu@x2S;$yyksH<X
zz;B+T`T02#>rVWPu3Nwx_26JKt7W75IZd_;%YG(xb9L<g^g_p@{Ic_}4GMP5IU5f<
z{oq=3-RRLGHqK~E1;GS`3G$J8#Sv|;Te5D5Zg7rt)LzCtiEl2;qpuw^gg+$K9hX`^
zzby0P_4e4#FZ*`<yr>X=Mtrm7&7@<Q57%sB3|2eZv^KXxE#tk`9X2Wb4-E5Hr>ih!
zUfk6b`{7k1(^Ph@E|y2f-V`k3x5!Bh{PL)Kzr_0X64g)U0VdmC1g0DgIP>hZ^1J0{
zpI3>hJa6ukn!ilTtvlL3nJrDPCt_Vt=$)6#*Vq0HQMux<Q|s2wW~C*X!kc(jG@Qv$
zy>zolXT$6{DN`9$H|2JlE6rHou_oraNY~r$rQtrtsh>BQs~rfJKGh=kZSI%Q#}gL1
zy<0w4_XN}KOvf<EhNR<S>sNDRPc>Is{{Q7^!y2yYWBOBeF<Q=>#WqWQc5|FbsnCxH
dRhzd2xTSsM&n!3^_DTe^8j)sT1~pQ^7yzU7G9mx~
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_Aligned.sortedByCoord.out.bam.bai 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_Aligned.sortedByCoord.out.bam.bai
deleted file mode 100644
index 431f324ff4c3b5672b01fb6e61651d319330949c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 96
zcmZ>A^kigYU|?WkU|{eRVqgHV85jaUTm}Y)=^P9U3=CeAAoA$qA|Od5jH(wR0RRyr
B1XKV3
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
deleted file mode 100644
index bd6da57..0000000
--- 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
+++ /dev/null
@@ -1,37 +0,0 @@
- 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
deleted file mode 100644
index 24bf24d5f8365b4fcab57b5346e4c86dc09c20fe..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 1486
zcmb2|=3rp}f&Xj_PR>jW?o3xh&*t4W;3@NOE|%C}eqpV;b=mEO4t_sx@8a7y`RL7c
zO=+7u8N5HK?DYM0qq@n{>#|wo9EO{Gvl+b2>?bLyek$HSea_#S$CY>eo&QJQ>O8D%
zFI`@wnBr)8@xrUL_&;YD9A#z-#@x6mFWDIRIIO(r@qIq)n`_L!s=ur<&C@&d`op9j
z%@Zdpv@|(fvk_!f2)blBpGotIn@zOG=b4MN)n_n^^R$I1ajw$anx*ZlvTRR->WXhp
z292UCH43iotGmDL-}MK#=6?J#aoU2spWU`kKMNUrShO}QM&IGG%yGeOySR)etMnBr
z7j^k+G<H@Wn5q$e<m96deHwq2=h!Qm$GKVw^a#c+I6mhEuSQnx#wi9fJa#NTy?-i?
zvS{4=51P*^gkzR*UwN-;Aspm<F`jqc>(s>$^L}WX{|*gU5b_~i<+W;6XyaD%MSJDq
zRtl|E{Tr7Zup)fg?TEdP>yGDC1qUgcKh-P_PWyQ%Z+eN}iR#}`CMRZkCrqt1o0O|!
zxZTA!LQ~mW#Qpa{9dV&$E$11J-j?F?)R4d5EOS#JKqT&+g`!pbk~bUpLeH$^T%GLP
zc_`y<{JQ^kADni|oH^|?<D}y+#}F6I>&w1*MBiQc`rY!!pZ%@(gq0h7%VrgN>OVDa
z{nBO`<2O%R6&!Xid}DNU{)Z#=2ZelDHtzq%FY;jHr{C=-mo+l?8D7ZOxxA!!LwKLr
z(~r|~lzP;fY<%L>gTjN4Z$D>qzB+r}TKnDK-`)9K#~3?pcAf|a0|R<G%4A+U%|8E%
zfyA-PT%2t}h0~gqnp$#GIeezy`#)Q1{zALZw+`aBwsM!e2<Y6KUU|a&LH2>`Nr?#y
zgDd0IuZu0@s=EID)&5SuzdtME_LobVe*EDnvUlgK&Ad9_FRZ(@U^#nxbKdswzU7Y-
z^RxQ5eee77uKnhgInz>a>Mp;XTHaGxZqd2Vu4|E(aeU<A*HM-6p>3-}#OG8`meS3B
zed$o8uE53{XWny7Jihb9Bn!VyI^Hfa>4v*(PG7v7CzSr9iD$lw-G<G)*7I{i+Bg5a
z`A^5n;kNnl#f~Mr*86k3cvZ5_zLj&uz4vnS=g+CPv;HX&D<u2q_O(|Z{?_F?eR$09
zUUWM5>e$2?Tdq2-iZOngd2-A8-cM6M&w0Rlu)E>@m$yvT4^-k72y15;KALNgroexZ
z=O*)k{k6M{YHrH+HGNvluwG$vQIO%(&mpI7Sw0Jmz3rqOXRW5a&)}63-v`|<bAMef
zp2)%2$a+Sh$fr=^$ov#0I|2ShfBH=y9Dka^^3?q<!+fpy4Sd@}-94FiE3=EVMR^|<
zx!&`-B(c0>Z|FWt#v6MK8#`tT+P?AKb@-P9t4)o+*#W*P6$g%u``+$9lC5Dc$(L8O
zZ$s<kbr-I!;EK%SnsiU&d7;Ry)myfm(w^Y_dv~$jhso!h9G=g3kjXuBpGmEEzi_1N
zzwpVQE`EO=_{A!w;{3bnhrGv`i~eTZxKkddxiWil_&zNzy~6LB>muSLA6s=@U1czJ
zp97!rhxzR$ZvAi6Qa!^M9{2OiGfj86(kq*BSE40t_Lpl?hxBh=?Vft`xJPBud)Bg;
zuTfcH4$lrrWbZL`lg>BT$bEWB$=0XVM{aDncKG1&rWjeK2My=*9!$TWuzU*#J44x?
zt-Icx-u*9io5|n3rTWJwCw_OU$Sc14k^80L%3hz+yd{M(#itWlr=1dcE_7+?l%<ER
zs%<<W{77ia5#c+Ty_Y>7-4@(Y`1z?4$NsjL_1l)+uPRmEbM&6=s+#(UZ=HL4^a7r2
zbyn40bF%lO?9!c&*h2lXQ?=&>o%NT!y7q#{@7IS!^$e_fX85t@-zoYv|HGsF{rh*v
z-rxRz_deqUbNjq^>nrQ8aG$()<$Jx8_^j8m51ROoEmib<kh?_pU~6rK+)nvx+Z%8H
a{Q7U#$$!#~HtQH}abo5)X$EEn7ytm~9nY-*
diff --git a/tests/test_alfa/results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam.bai
deleted file mode 100644
index bb9718376bfaeeddb2ae1aecc484e09daff86ec3..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 96
zcmZ>A^kigYU|?WkU|{eRVqgHV85lf3Tm}Y)O{@$I3=CeAAoA$qTp&p#jH(wR0RR<|
B1Y!UH
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
deleted file mode 100644
index 5cd0686..0000000
--- 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
+++ /dev/null
@@ -1,37 +0,0 @@
- 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_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt b/tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
index 2d6cebe..81ed9d3 100644
--- a/tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
+++ b/tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
@@ -1 +1 @@
-1-10000-20000 10001
+Chr1 1500
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 036534b..9590555 100755
--- a/tests/test_alfa/test.sh
+++ b/tests/test_alfa/test.sh
@@ -26,16 +26,14 @@ cd $script_dir
# Run tests
snakemake \
--snakefile="../../Snakefile" \
- --configfile="../input_files/config.yaml" \
+ --configfile="input_files/config.yaml" \
--cores=4 \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
--use-conda \
- --singularity-args="--bind ${PWD}/../input_files" \
+ --singularity-args="--bind ${PWD}" \
--verbose \
- results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/ALFA_plots.Categories.pdf \
- results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/ALFA_plots.Categories.pdf \
results/ALFA/ALFA_plots.Categories.pdf
# Check md5 sum of some output files
--
GitLab