From 82c4dcea727fdd05531f05d89f9dd04b6a64996f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?BIOPZ-B=C3=B6rsch=20Anastasiya?=
<anastasiya.boersch@unibas.ch>
Date: Mon, 15 Jun 2020 12:18:44 +0200
Subject: [PATCH] refactor: rename LabKey/input table column
---
images/dag_test_workflow.svg | 128 +++++++++---------
scripts/prepare_inputs.dict.tsv | 2 +-
scripts/prepare_inputs.py | 4 +-
.../synthetic_split_lane1.mate_1.fastq.gz | Bin 0 -> 445 bytes
.../synthetic_split_lane1.mate_2.fastq.gz | Bin 0 -> 442 bytes
.../synthetic_split_lane2.mate_1.fastq.gz | Bin 0 -> 415 bytes
.../synthetic_split_lane2.mate_2.fastq.gz | Bin 0 -> 407 bytes
tests/input_files/samples_concat.tsv | 7 +
.../synthetic_split_lane1.mate_1.fastq.gz | Bin 0 -> 445 bytes
.../synthetic_split_lane2.mate_1.fastq.gz | Bin 0 -> 415 bytes
.../test.sh | 2 +-
.../input_table.tsv | 2 +-
12 files changed, 76 insertions(+), 69 deletions(-)
create mode 100644 tests/input_files/pe_lane1/synthetic_split_lane1.mate_1.fastq.gz
create mode 100644 tests/input_files/pe_lane1/synthetic_split_lane1.mate_2.fastq.gz
create mode 100644 tests/input_files/pe_lane2/synthetic_split_lane2.mate_1.fastq.gz
create mode 100644 tests/input_files/pe_lane2/synthetic_split_lane2.mate_2.fastq.gz
create mode 100644 tests/input_files/samples_concat.tsv
create mode 100644 tests/input_files/se_lane1/synthetic_split_lane1.mate_1.fastq.gz
create mode 100644 tests/input_files/se_lane2/synthetic_split_lane2.mate_1.fastq.gz
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index bcd33c5..2a883ae 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="#5673d8" stroke-width="2" d="M1486.5,-36C1486.5,-36 1456.5,-36 1456.5,-36 1450.5,-36 1444.5,-30 1444.5,-24 1444.5,-24 1444.5,-12 1444.5,-12 1444.5,-6 1450.5,0 1456.5,0 1456.5,0 1486.5,0 1486.5,0 1492.5,0 1498.5,-6 1498.5,-12 1498.5,-12 1498.5,-24 1498.5,-24 1498.5,-30 1492.5,-36 1486.5,-36"/>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M1486.5,-36C1486.5,-36 1456.5,-36 1456.5,-36 1450.5,-36 1444.5,-30 1444.5,-24 1444.5,-24 1444.5,-12 1444.5,-12 1444.5,-6 1450.5,0 1456.5,0 1456.5,0 1486.5,0 1486.5,0 1492.5,0 1498.5,-6 1498.5,-12 1498.5,-12 1498.5,-24 1498.5,-24 1498.5,-30 1492.5,-36 1486.5,-36"/>
<text text-anchor="middle" x="1471.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M601.5,-108C601.5,-108 537.5,-108 537.5,-108 531.5,-108 525.5,-102 525.5,-96 525.5,-96 525.5,-84 525.5,-84 525.5,-78 531.5,-72 537.5,-72 537.5,-72 601.5,-72 601.5,-72 607.5,-72 613.5,-78 613.5,-84 613.5,-84 613.5,-96 613.5,-96 613.5,-102 607.5,-108 601.5,-108"/>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M601.5,-108C601.5,-108 537.5,-108 537.5,-108 531.5,-108 525.5,-102 525.5,-96 525.5,-96 525.5,-84 525.5,-84 525.5,-78 531.5,-72 537.5,-72 537.5,-72 601.5,-72 601.5,-72 607.5,-72 613.5,-78 613.5,-84 613.5,-84 613.5,-96 613.5,-96 613.5,-102 607.5,-108 601.5,-108"/>
<text text-anchor="middle" x="569.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">multiqc_report</text>
</g>
<!-- 1->0 -->
@@ -30,7 +30,7 @@
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1126,-252C1126,-252 1057,-252 1057,-252 1051,-252 1045,-246 1045,-240 1045,-240 1045,-228 1045,-228 1045,-222 1051,-216 1057,-216 1057,-216 1126,-216 1126,-216 1132,-216 1138,-222 1138,-228 1138,-228 1138,-240 1138,-240 1138,-246 1132,-252 1126,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1126,-252C1126,-252 1057,-252 1057,-252 1051,-252 1045,-246 1045,-240 1045,-240 1045,-228 1045,-228 1045,-222 1051,-216 1057,-216 1057,-216 1126,-216 1126,-216 1132,-216 1138,-222 1138,-228 1138,-228 1138,-240 1138,-240 1138,-246 1132,-252 1126,-252"/>
<text text-anchor="middle" x="1091.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 2->0 -->
@@ -42,7 +42,7 @@
<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1617,-252C1617,-252 1548,-252 1548,-252 1542,-252 1536,-246 1536,-240 1536,-240 1536,-228 1536,-228 1536,-222 1542,-216 1548,-216 1548,-216 1617,-216 1617,-216 1623,-216 1629,-222 1629,-228 1629,-228 1629,-240 1629,-240 1629,-246 1623,-252 1617,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1617,-252C1617,-252 1548,-252 1548,-252 1542,-252 1536,-246 1536,-240 1536,-240 1536,-228 1536,-228 1536,-222 1542,-216 1548,-216 1548,-216 1617,-216 1617,-216 1623,-216 1629,-222 1629,-228 1629,-228 1629,-240 1629,-240 1629,-246 1623,-252 1617,-252"/>
<text text-anchor="middle" x="1582.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 3->0 -->
@@ -54,7 +54,7 @@
<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1506,-252C1506,-252 1437,-252 1437,-252 1431,-252 1425,-246 1425,-240 1425,-240 1425,-228 1425,-228 1425,-222 1431,-216 1437,-216 1437,-216 1506,-216 1506,-216 1512,-216 1518,-222 1518,-228 1518,-228 1518,-240 1518,-240 1518,-246 1512,-252 1506,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1506,-252C1506,-252 1437,-252 1437,-252 1431,-252 1425,-246 1425,-240 1425,-240 1425,-228 1425,-228 1425,-222 1431,-216 1437,-216 1437,-216 1506,-216 1506,-216 1512,-216 1518,-222 1518,-228 1518,-228 1518,-240 1518,-240 1518,-246 1512,-252 1506,-252"/>
<text text-anchor="middle" x="1471.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 4->0 -->
@@ -66,7 +66,7 @@
<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1728,-252C1728,-252 1659,-252 1659,-252 1653,-252 1647,-246 1647,-240 1647,-240 1647,-228 1647,-228 1647,-222 1653,-216 1659,-216 1659,-216 1728,-216 1728,-216 1734,-216 1740,-222 1740,-228 1740,-228 1740,-240 1740,-240 1740,-246 1734,-252 1728,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1728,-252C1728,-252 1659,-252 1659,-252 1653,-252 1647,-246 1647,-240 1647,-240 1647,-228 1647,-228 1647,-222 1653,-216 1659,-216 1659,-216 1728,-216 1728,-216 1734,-216 1740,-222 1740,-228 1740,-228 1740,-240 1740,-240 1740,-246 1734,-252 1728,-252"/>
<text text-anchor="middle" x="1693.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 5->0 -->
@@ -78,7 +78,7 @@
<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1839,-252C1839,-252 1770,-252 1770,-252 1764,-252 1758,-246 1758,-240 1758,-240 1758,-228 1758,-228 1758,-222 1764,-216 1770,-216 1770,-216 1839,-216 1839,-216 1845,-216 1851,-222 1851,-228 1851,-228 1851,-240 1851,-240 1851,-246 1845,-252 1839,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1839,-252C1839,-252 1770,-252 1770,-252 1764,-252 1758,-246 1758,-240 1758,-240 1758,-228 1758,-228 1758,-222 1764,-216 1770,-216 1770,-216 1839,-216 1839,-216 1845,-216 1851,-222 1851,-228 1851,-228 1851,-240 1851,-240 1851,-246 1845,-252 1839,-252"/>
<text text-anchor="middle" x="1804.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 6->0 -->
@@ -90,7 +90,7 @@
<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M2241,-252C2241,-252 2172,-252 2172,-252 2166,-252 2160,-246 2160,-240 2160,-240 2160,-228 2160,-228 2160,-222 2166,-216 2172,-216 2172,-216 2241,-216 2241,-216 2247,-216 2253,-222 2253,-228 2253,-228 2253,-240 2253,-240 2253,-246 2247,-252 2241,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M2241,-252C2241,-252 2172,-252 2172,-252 2166,-252 2160,-246 2160,-240 2160,-240 2160,-228 2160,-228 2160,-222 2166,-216 2172,-216 2172,-216 2241,-216 2241,-216 2247,-216 2253,-222 2253,-228 2253,-228 2253,-240 2253,-240 2253,-246 2247,-252 2241,-252"/>
<text text-anchor="middle" x="2206.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 7->0 -->
@@ -102,7 +102,7 @@
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M2061,-252C2061,-252 1992,-252 1992,-252 1986,-252 1980,-246 1980,-240 1980,-240 1980,-228 1980,-228 1980,-222 1986,-216 1992,-216 1992,-216 2061,-216 2061,-216 2067,-216 2073,-222 2073,-228 2073,-228 2073,-240 2073,-240 2073,-246 2067,-252 2061,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M2061,-252C2061,-252 1992,-252 1992,-252 1986,-252 1980,-246 1980,-240 1980,-240 1980,-228 1980,-228 1980,-222 1986,-216 1992,-216 1992,-216 2061,-216 2061,-216 2067,-216 2073,-222 2073,-228 2073,-228 2073,-240 2073,-240 2073,-246 2067,-252 2061,-252"/>
<text text-anchor="middle" x="2026.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 8->0 -->
@@ -114,7 +114,7 @@
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1950,-252C1950,-252 1881,-252 1881,-252 1875,-252 1869,-246 1869,-240 1869,-240 1869,-228 1869,-228 1869,-222 1875,-216 1881,-216 1881,-216 1950,-216 1950,-216 1956,-216 1962,-222 1962,-228 1962,-228 1962,-240 1962,-240 1962,-246 1956,-252 1950,-252"/>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1950,-252C1950,-252 1881,-252 1881,-252 1875,-252 1869,-246 1869,-240 1869,-240 1869,-228 1869,-228 1869,-222 1875,-216 1881,-216 1881,-216 1950,-216 1950,-216 1956,-216 1962,-222 1962,-228 1962,-228 1962,-240 1962,-240 1962,-246 1956,-252 1950,-252"/>
<text text-anchor="middle" x="1915.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
<!-- 9->0 -->
@@ -126,7 +126,7 @@
<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M771.5,-108C771.5,-108 643.5,-108 643.5,-108 637.5,-108 631.5,-102 631.5,-96 631.5,-96 631.5,-84 631.5,-84 631.5,-78 637.5,-72 643.5,-72 643.5,-72 771.5,-72 771.5,-72 777.5,-72 783.5,-78 783.5,-84 783.5,-84 783.5,-96 783.5,-96 783.5,-102 777.5,-108 771.5,-108"/>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M771.5,-108C771.5,-108 643.5,-108 643.5,-108 637.5,-108 631.5,-102 631.5,-96 631.5,-96 631.5,-84 631.5,-84 631.5,-78 637.5,-72 643.5,-72 643.5,-72 771.5,-72 771.5,-72 777.5,-72 783.5,-78 783.5,-84 783.5,-84 783.5,-96 783.5,-96 783.5,-102 777.5,-108 771.5,-108"/>
<text text-anchor="middle" x="707.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="707.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
</g>
@@ -139,7 +139,7 @@
<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M951,-108C951,-108 814,-108 814,-108 808,-108 802,-102 802,-96 802,-96 802,-84 802,-84 802,-78 808,-72 814,-72 814,-72 951,-72 951,-72 957,-72 963,-78 963,-84 963,-84 963,-96 963,-96 963,-102 957,-108 951,-108"/>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M951,-108C951,-108 814,-108 814,-108 808,-108 802,-102 802,-96 802,-96 802,-84 802,-84 802,-78 808,-72 814,-72 814,-72 951,-72 951,-72 957,-72 963,-78 963,-84 963,-84 963,-96 963,-96 963,-102 957,-108 951,-108"/>
<text text-anchor="middle" x="882.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="882.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
</g>
@@ -152,7 +152,7 @@
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M1143.5,-108C1143.5,-108 993.5,-108 993.5,-108 987.5,-108 981.5,-102 981.5,-96 981.5,-96 981.5,-84 981.5,-84 981.5,-78 987.5,-72 993.5,-72 993.5,-72 1143.5,-72 1143.5,-72 1149.5,-72 1155.5,-78 1155.5,-84 1155.5,-84 1155.5,-96 1155.5,-96 1155.5,-102 1149.5,-108 1143.5,-108"/>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1143.5,-108C1143.5,-108 993.5,-108 993.5,-108 987.5,-108 981.5,-102 981.5,-96 981.5,-96 981.5,-84 981.5,-84 981.5,-78 987.5,-72 993.5,-72 993.5,-72 1143.5,-72 1143.5,-72 1149.5,-72 1155.5,-78 1155.5,-84 1155.5,-84 1155.5,-96 1155.5,-96 1155.5,-102 1149.5,-108 1143.5,-108"/>
<text text-anchor="middle" x="1068.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="1068.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
</g>
@@ -165,7 +165,7 @@
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M1335.5,-108C1335.5,-108 1185.5,-108 1185.5,-108 1179.5,-108 1173.5,-102 1173.5,-96 1173.5,-96 1173.5,-84 1173.5,-84 1173.5,-78 1179.5,-72 1185.5,-72 1185.5,-72 1335.5,-72 1335.5,-72 1341.5,-72 1347.5,-78 1347.5,-84 1347.5,-84 1347.5,-96 1347.5,-96 1347.5,-102 1341.5,-108 1335.5,-108"/>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1335.5,-108C1335.5,-108 1185.5,-108 1185.5,-108 1179.5,-108 1173.5,-102 1173.5,-96 1173.5,-96 1173.5,-84 1173.5,-84 1173.5,-78 1179.5,-72 1185.5,-72 1185.5,-72 1335.5,-72 1335.5,-72 1341.5,-72 1347.5,-78 1347.5,-84 1347.5,-84 1347.5,-96 1347.5,-96 1347.5,-102 1341.5,-108 1335.5,-108"/>
<text text-anchor="middle" x="1260.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="1260.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
</g>
@@ -178,7 +178,7 @@
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M176.5,-612C176.5,-612 146.5,-612 146.5,-612 140.5,-612 134.5,-606 134.5,-600 134.5,-600 134.5,-588 134.5,-588 134.5,-582 140.5,-576 146.5,-576 146.5,-576 176.5,-576 176.5,-576 182.5,-576 188.5,-582 188.5,-588 188.5,-588 188.5,-600 188.5,-600 188.5,-606 182.5,-612 176.5,-612"/>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M176.5,-612C176.5,-612 146.5,-612 146.5,-612 140.5,-612 134.5,-606 134.5,-600 134.5,-600 134.5,-588 134.5,-588 134.5,-582 140.5,-576 146.5,-576 146.5,-576 176.5,-576 176.5,-576 182.5,-576 188.5,-582 188.5,-588 188.5,-588 188.5,-600 188.5,-600 188.5,-606 182.5,-612 176.5,-612"/>
<text text-anchor="middle" x="161.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
</g>
<!-- 14->1 -->
@@ -190,7 +190,7 @@
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M231.5,-686.5C231.5,-686.5 201.5,-686.5 201.5,-686.5 195.5,-686.5 189.5,-680.5 189.5,-674.5 189.5,-674.5 189.5,-662.5 189.5,-662.5 189.5,-656.5 195.5,-650.5 201.5,-650.5 201.5,-650.5 231.5,-650.5 231.5,-650.5 237.5,-650.5 243.5,-656.5 243.5,-662.5 243.5,-662.5 243.5,-674.5 243.5,-674.5 243.5,-680.5 237.5,-686.5 231.5,-686.5"/>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M231.5,-686.5C231.5,-686.5 201.5,-686.5 201.5,-686.5 195.5,-686.5 189.5,-680.5 189.5,-674.5 189.5,-674.5 189.5,-662.5 189.5,-662.5 189.5,-656.5 195.5,-650.5 201.5,-650.5 201.5,-650.5 231.5,-650.5 231.5,-650.5 237.5,-650.5 243.5,-656.5 243.5,-662.5 243.5,-662.5 243.5,-674.5 243.5,-674.5 243.5,-680.5 237.5,-686.5 231.5,-686.5"/>
<text text-anchor="middle" x="216.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
</g>
<!-- 15->1 -->
@@ -202,7 +202,7 @@
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1035.5,-761C1035.5,-761 1005.5,-761 1005.5,-761 999.5,-761 993.5,-755 993.5,-749 993.5,-749 993.5,-737 993.5,-737 993.5,-731 999.5,-725 1005.5,-725 1005.5,-725 1035.5,-725 1035.5,-725 1041.5,-725 1047.5,-731 1047.5,-737 1047.5,-737 1047.5,-749 1047.5,-749 1047.5,-755 1041.5,-761 1035.5,-761"/>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M1035.5,-761C1035.5,-761 1005.5,-761 1005.5,-761 999.5,-761 993.5,-755 993.5,-749 993.5,-749 993.5,-737 993.5,-737 993.5,-731 999.5,-725 1005.5,-725 1005.5,-725 1035.5,-725 1035.5,-725 1041.5,-725 1047.5,-731 1047.5,-737 1047.5,-737 1047.5,-749 1047.5,-749 1047.5,-755 1041.5,-761 1035.5,-761"/>
<text text-anchor="middle" x="1020.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
</g>
<!-- 16->1 -->
@@ -214,7 +214,7 @@
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M457,-252C457,-252 294,-252 294,-252 288,-252 282,-246 282,-240 282,-240 282,-228 282,-228 282,-222 288,-216 294,-216 294,-216 457,-216 457,-216 463,-216 469,-222 469,-228 469,-228 469,-240 469,-240 469,-246 463,-252 457,-252"/>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M457,-252C457,-252 294,-252 294,-252 288,-252 282,-246 282,-240 282,-240 282,-228 282,-228 282,-222 288,-216 294,-216 294,-216 457,-216 457,-216 463,-216 469,-222 469,-228 469,-228 469,-240 469,-240 469,-246 463,-252 457,-252"/>
<text text-anchor="middle" x="375.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
</g>
<!-- 17->1 -->
@@ -226,7 +226,7 @@
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M645.5,-252C645.5,-252 499.5,-252 499.5,-252 493.5,-252 487.5,-246 487.5,-240 487.5,-240 487.5,-228 487.5,-228 487.5,-222 493.5,-216 499.5,-216 499.5,-216 645.5,-216 645.5,-216 651.5,-216 657.5,-222 657.5,-228 657.5,-228 657.5,-240 657.5,-240 657.5,-246 651.5,-252 645.5,-252"/>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M645.5,-252C645.5,-252 499.5,-252 499.5,-252 493.5,-252 487.5,-246 487.5,-240 487.5,-240 487.5,-228 487.5,-228 487.5,-222 493.5,-216 499.5,-216 499.5,-216 645.5,-216 645.5,-216 651.5,-216 657.5,-222 657.5,-228 657.5,-228 657.5,-240 657.5,-240 657.5,-246 651.5,-252 645.5,-252"/>
<text text-anchor="middle" x="572.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
</g>
<!-- 18->1 -->
@@ -238,7 +238,7 @@
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M711.5,-180C711.5,-180 641.5,-180 641.5,-180 635.5,-180 629.5,-174 629.5,-168 629.5,-168 629.5,-156 629.5,-156 629.5,-150 635.5,-144 641.5,-144 641.5,-144 711.5,-144 711.5,-144 717.5,-144 723.5,-150 723.5,-156 723.5,-156 723.5,-168 723.5,-168 723.5,-174 717.5,-180 711.5,-180"/>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M711.5,-180C711.5,-180 641.5,-180 641.5,-180 635.5,-180 629.5,-174 629.5,-168 629.5,-168 629.5,-156 629.5,-156 629.5,-150 635.5,-144 641.5,-144 641.5,-144 711.5,-144 711.5,-144 717.5,-144 723.5,-150 723.5,-156 723.5,-156 723.5,-168 723.5,-168 723.5,-174 717.5,-180 711.5,-180"/>
<text text-anchor="middle" x="676.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
</g>
<!-- 19->1 -->
@@ -250,7 +250,7 @@
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M1412,-180C1412,-180 1325,-180 1325,-180 1319,-180 1313,-174 1313,-168 1313,-168 1313,-156 1313,-156 1313,-150 1319,-144 1325,-144 1325,-144 1412,-144 1412,-144 1418,-144 1424,-150 1424,-156 1424,-156 1424,-168 1424,-168 1424,-174 1418,-180 1412,-180"/>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1412,-180C1412,-180 1325,-180 1325,-180 1319,-180 1313,-174 1313,-168 1313,-168 1313,-156 1313,-156 1313,-150 1319,-144 1325,-144 1325,-144 1412,-144 1412,-144 1418,-144 1424,-150 1424,-156 1424,-156 1424,-168 1424,-168 1424,-174 1418,-180 1412,-180"/>
<text text-anchor="middle" x="1368.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
</g>
<!-- 20->1 -->
@@ -262,7 +262,7 @@
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M138,-180C138,-180 31,-180 31,-180 25,-180 19,-174 19,-168 19,-168 19,-156 19,-156 19,-150 25,-144 31,-144 31,-144 138,-144 138,-144 144,-144 150,-150 150,-156 150,-156 150,-168 150,-168 150,-174 144,-180 138,-180"/>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M138,-180C138,-180 31,-180 31,-180 25,-180 19,-174 19,-168 19,-168 19,-156 19,-156 19,-150 25,-144 31,-144 31,-144 138,-144 138,-144 144,-144 150,-150 150,-156 150,-156 150,-168 150,-168 150,-174 144,-180 138,-180"/>
<text text-anchor="middle" x="84.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
</g>
<!-- 21->1 -->
@@ -274,7 +274,7 @@
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M926.5,-324C926.5,-324 860.5,-324 860.5,-324 854.5,-324 848.5,-318 848.5,-312 848.5,-312 848.5,-300 848.5,-300 848.5,-294 854.5,-288 860.5,-288 860.5,-288 926.5,-288 926.5,-288 932.5,-288 938.5,-294 938.5,-300 938.5,-300 938.5,-312 938.5,-312 938.5,-318 932.5,-324 926.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M926.5,-324C926.5,-324 860.5,-324 860.5,-324 854.5,-324 848.5,-318 848.5,-312 848.5,-312 848.5,-300 848.5,-300 848.5,-294 854.5,-288 860.5,-288 860.5,-288 926.5,-288 926.5,-288 932.5,-288 938.5,-294 938.5,-300 938.5,-300 938.5,-312 938.5,-312 938.5,-318 932.5,-324 926.5,-324"/>
<text text-anchor="middle" x="893.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="893.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
</g>
@@ -287,7 +287,7 @@
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1730,-689C1730,-689 1615,-689 1615,-689 1609,-689 1603,-683 1603,-677 1603,-677 1603,-660 1603,-660 1603,-654 1609,-648 1615,-648 1615,-648 1730,-648 1730,-648 1736,-648 1742,-654 1742,-660 1742,-660 1742,-677 1742,-677 1742,-683 1736,-689 1730,-689"/>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1730,-689C1730,-689 1615,-689 1615,-689 1609,-689 1603,-683 1603,-677 1603,-677 1603,-660 1603,-660 1603,-654 1609,-648 1615,-648 1615,-648 1730,-648 1730,-648 1736,-648 1742,-654 1742,-660 1742,-660 1742,-677 1742,-677 1742,-683 1736,-689 1730,-689"/>
<text text-anchor="middle" x="1672.5" y="-677" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
<text text-anchor="middle" x="1672.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
<text text-anchor="middle" x="1672.5" y="-655" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
@@ -343,7 +343,7 @@
<!-- 46 -->
<g id="node47" class="node">
<title>46</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M921,-252C921,-252 824,-252 824,-252 818,-252 812,-246 812,-240 812,-240 812,-228 812,-228 812,-222 818,-216 824,-216 824,-216 921,-216 921,-216 927,-216 933,-222 933,-228 933,-228 933,-240 933,-240 933,-246 927,-252 921,-252"/>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M921,-252C921,-252 824,-252 824,-252 818,-252 812,-246 812,-240 812,-240 812,-228 812,-228 812,-222 818,-216 824,-216 824,-216 921,-216 921,-216 927,-216 933,-222 933,-228 933,-228 933,-240 933,-240 933,-246 927,-252 921,-252"/>
<text text-anchor="middle" x="872.5" y="-237" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
<text text-anchor="middle" x="872.5" y="-226" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
</g>
@@ -356,7 +356,7 @@
<!-- 59 -->
<g id="node60" class="node">
<title>59</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M741,-612C741,-612 640,-612 640,-612 634,-612 628,-606 628,-600 628,-600 628,-588 628,-588 628,-582 634,-576 640,-576 640,-576 741,-576 741,-576 747,-576 753,-582 753,-588 753,-588 753,-600 753,-600 753,-606 747,-612 741,-612"/>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M741,-612C741,-612 640,-612 640,-612 634,-612 628,-606 628,-600 628,-600 628,-588 628,-588 628,-582 634,-576 640,-576 640,-576 741,-576 741,-576 747,-576 753,-582 753,-588 753,-588 753,-600 753,-600 753,-606 747,-612 741,-612"/>
<text text-anchor="middle" x="690.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
<!-- 23->59 -->
@@ -368,7 +368,7 @@
<!-- 62 -->
<g id="node63" class="node">
<title>62</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1238,-612C1238,-612 1155,-612 1155,-612 1149,-612 1143,-606 1143,-600 1143,-600 1143,-588 1143,-588 1143,-582 1149,-576 1155,-576 1155,-576 1238,-576 1238,-576 1244,-576 1250,-582 1250,-588 1250,-588 1250,-600 1250,-600 1250,-606 1244,-612 1238,-612"/>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M1238,-612C1238,-612 1155,-612 1155,-612 1149,-612 1143,-606 1143,-600 1143,-600 1143,-588 1143,-588 1143,-582 1149,-576 1155,-576 1155,-576 1238,-576 1238,-576 1244,-576 1250,-582 1250,-588 1250,-588 1250,-600 1250,-600 1250,-606 1244,-612 1238,-612"/>
<text text-anchor="middle" x="1196.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
</g>
<!-- 23->62 -->
@@ -380,7 +380,7 @@
<!-- 64 -->
<g id="node65" class="node">
<title>64</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M1320.5,-396C1320.5,-396 1228.5,-396 1228.5,-396 1222.5,-396 1216.5,-390 1216.5,-384 1216.5,-384 1216.5,-372 1216.5,-372 1216.5,-366 1222.5,-360 1228.5,-360 1228.5,-360 1320.5,-360 1320.5,-360 1326.5,-360 1332.5,-366 1332.5,-372 1332.5,-372 1332.5,-384 1332.5,-384 1332.5,-390 1326.5,-396 1320.5,-396"/>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1320.5,-396C1320.5,-396 1228.5,-396 1228.5,-396 1222.5,-396 1216.5,-390 1216.5,-384 1216.5,-384 1216.5,-372 1216.5,-372 1216.5,-366 1222.5,-360 1228.5,-360 1228.5,-360 1320.5,-360 1320.5,-360 1326.5,-360 1332.5,-366 1332.5,-372 1332.5,-372 1332.5,-384 1332.5,-384 1332.5,-390 1326.5,-396 1320.5,-396"/>
<text text-anchor="middle" x="1274.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
</g>
<!-- 23->64 -->
@@ -392,7 +392,7 @@
<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1214.5,-324C1214.5,-324 1148.5,-324 1148.5,-324 1142.5,-324 1136.5,-318 1136.5,-312 1136.5,-312 1136.5,-300 1136.5,-300 1136.5,-294 1142.5,-288 1148.5,-288 1148.5,-288 1214.5,-288 1214.5,-288 1220.5,-288 1226.5,-294 1226.5,-300 1226.5,-300 1226.5,-312 1226.5,-312 1226.5,-318 1220.5,-324 1214.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1214.5,-324C1214.5,-324 1148.5,-324 1148.5,-324 1142.5,-324 1136.5,-318 1136.5,-312 1136.5,-312 1136.5,-300 1136.5,-300 1136.5,-294 1142.5,-288 1148.5,-288 1148.5,-288 1214.5,-288 1214.5,-288 1220.5,-288 1226.5,-294 1226.5,-300 1226.5,-300 1226.5,-312 1226.5,-312 1226.5,-318 1220.5,-324 1214.5,-324"/>
<text text-anchor="middle" x="1181.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="1181.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
</g>
@@ -405,7 +405,7 @@
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1106.5,-324C1106.5,-324 1040.5,-324 1040.5,-324 1034.5,-324 1028.5,-318 1028.5,-312 1028.5,-312 1028.5,-300 1028.5,-300 1028.5,-294 1034.5,-288 1040.5,-288 1040.5,-288 1106.5,-288 1106.5,-288 1112.5,-288 1118.5,-294 1118.5,-300 1118.5,-300 1118.5,-312 1118.5,-312 1118.5,-318 1112.5,-324 1106.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1106.5,-324C1106.5,-324 1040.5,-324 1040.5,-324 1034.5,-324 1028.5,-318 1028.5,-312 1028.5,-312 1028.5,-300 1028.5,-300 1028.5,-294 1034.5,-288 1040.5,-288 1040.5,-288 1106.5,-288 1106.5,-288 1112.5,-288 1118.5,-294 1118.5,-300 1118.5,-300 1118.5,-312 1118.5,-312 1118.5,-318 1112.5,-324 1106.5,-324"/>
<text text-anchor="middle" x="1073.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="1073.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
</g>
@@ -418,7 +418,7 @@
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1470.5,-324C1470.5,-324 1404.5,-324 1404.5,-324 1398.5,-324 1392.5,-318 1392.5,-312 1392.5,-312 1392.5,-300 1392.5,-300 1392.5,-294 1398.5,-288 1404.5,-288 1404.5,-288 1470.5,-288 1470.5,-288 1476.5,-288 1482.5,-294 1482.5,-300 1482.5,-300 1482.5,-312 1482.5,-312 1482.5,-318 1476.5,-324 1470.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1470.5,-324C1470.5,-324 1404.5,-324 1404.5,-324 1398.5,-324 1392.5,-318 1392.5,-312 1392.5,-312 1392.5,-300 1392.5,-300 1392.5,-294 1398.5,-288 1404.5,-288 1404.5,-288 1470.5,-288 1470.5,-288 1476.5,-288 1482.5,-294 1482.5,-300 1482.5,-300 1482.5,-312 1482.5,-312 1482.5,-318 1476.5,-324 1470.5,-324"/>
<text text-anchor="middle" x="1437.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="1437.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
</g>
@@ -431,7 +431,7 @@
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1838.5,-324C1838.5,-324 1772.5,-324 1772.5,-324 1766.5,-324 1760.5,-318 1760.5,-312 1760.5,-312 1760.5,-300 1760.5,-300 1760.5,-294 1766.5,-288 1772.5,-288 1772.5,-288 1838.5,-288 1838.5,-288 1844.5,-288 1850.5,-294 1850.5,-300 1850.5,-300 1850.5,-312 1850.5,-312 1850.5,-318 1844.5,-324 1838.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1838.5,-324C1838.5,-324 1772.5,-324 1772.5,-324 1766.5,-324 1760.5,-318 1760.5,-312 1760.5,-312 1760.5,-300 1760.5,-300 1760.5,-294 1766.5,-288 1772.5,-288 1772.5,-288 1838.5,-288 1838.5,-288 1844.5,-288 1850.5,-294 1850.5,-300 1850.5,-300 1850.5,-312 1850.5,-312 1850.5,-318 1844.5,-324 1838.5,-324"/>
<text text-anchor="middle" x="1805.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="1805.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
</g>
@@ -444,7 +444,7 @@
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M2239.5,-324C2239.5,-324 2173.5,-324 2173.5,-324 2167.5,-324 2161.5,-318 2161.5,-312 2161.5,-312 2161.5,-300 2161.5,-300 2161.5,-294 2167.5,-288 2173.5,-288 2173.5,-288 2239.5,-288 2239.5,-288 2245.5,-288 2251.5,-294 2251.5,-300 2251.5,-300 2251.5,-312 2251.5,-312 2251.5,-318 2245.5,-324 2239.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M2239.5,-324C2239.5,-324 2173.5,-324 2173.5,-324 2167.5,-324 2161.5,-318 2161.5,-312 2161.5,-312 2161.5,-300 2161.5,-300 2161.5,-294 2167.5,-288 2173.5,-288 2173.5,-288 2239.5,-288 2239.5,-288 2245.5,-288 2251.5,-294 2251.5,-300 2251.5,-300 2251.5,-312 2251.5,-312 2251.5,-318 2245.5,-324 2239.5,-324"/>
<text text-anchor="middle" x="2206.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="2206.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
</g>
@@ -457,7 +457,7 @@
<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M2055.5,-324C2055.5,-324 1989.5,-324 1989.5,-324 1983.5,-324 1977.5,-318 1977.5,-312 1977.5,-312 1977.5,-300 1977.5,-300 1977.5,-294 1983.5,-288 1989.5,-288 1989.5,-288 2055.5,-288 2055.5,-288 2061.5,-288 2067.5,-294 2067.5,-300 2067.5,-300 2067.5,-312 2067.5,-312 2067.5,-318 2061.5,-324 2055.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M2055.5,-324C2055.5,-324 1989.5,-324 1989.5,-324 1983.5,-324 1977.5,-318 1977.5,-312 1977.5,-312 1977.5,-300 1977.5,-300 1977.5,-294 1983.5,-288 1989.5,-288 1989.5,-288 2055.5,-288 2055.5,-288 2061.5,-288 2067.5,-294 2067.5,-300 2067.5,-300 2067.5,-312 2067.5,-312 2067.5,-318 2061.5,-324 2055.5,-324"/>
<text text-anchor="middle" x="2022.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="2022.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
</g>
@@ -470,7 +470,7 @@
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1947.5,-324C1947.5,-324 1881.5,-324 1881.5,-324 1875.5,-324 1869.5,-318 1869.5,-312 1869.5,-312 1869.5,-300 1869.5,-300 1869.5,-294 1875.5,-288 1881.5,-288 1881.5,-288 1947.5,-288 1947.5,-288 1953.5,-288 1959.5,-294 1959.5,-300 1959.5,-300 1959.5,-312 1959.5,-312 1959.5,-318 1953.5,-324 1947.5,-324"/>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1947.5,-324C1947.5,-324 1881.5,-324 1881.5,-324 1875.5,-324 1869.5,-318 1869.5,-312 1869.5,-312 1869.5,-300 1869.5,-300 1869.5,-294 1875.5,-288 1881.5,-288 1881.5,-288 1947.5,-288 1947.5,-288 1953.5,-288 1959.5,-294 1959.5,-300 1959.5,-300 1959.5,-312 1959.5,-312 1959.5,-318 1953.5,-324 1947.5,-324"/>
<text text-anchor="middle" x="1914.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
<text text-anchor="middle" x="1914.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
</g>
@@ -483,7 +483,7 @@
<!-- 31 -->
<g id="node32" class="node">
<title>31</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M941.5,-180C941.5,-180 823.5,-180 823.5,-180 817.5,-180 811.5,-174 811.5,-168 811.5,-168 811.5,-156 811.5,-156 811.5,-150 817.5,-144 823.5,-144 823.5,-144 941.5,-144 941.5,-144 947.5,-144 953.5,-150 953.5,-156 953.5,-156 953.5,-168 953.5,-168 953.5,-174 947.5,-180 941.5,-180"/>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M941.5,-180C941.5,-180 823.5,-180 823.5,-180 817.5,-180 811.5,-174 811.5,-168 811.5,-168 811.5,-156 811.5,-156 811.5,-150 817.5,-144 823.5,-144 823.5,-144 941.5,-144 941.5,-144 947.5,-144 953.5,-150 953.5,-156 953.5,-156 953.5,-168 953.5,-168 953.5,-174 947.5,-180 941.5,-180"/>
<text text-anchor="middle" x="882.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
</g>
<!-- 31->10 -->
@@ -513,7 +513,7 @@
<!-- 32 -->
<g id="node33" class="node">
<title>32</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M1085,-180C1085,-180 984,-180 984,-180 978,-180 972,-174 972,-168 972,-168 972,-156 972,-156 972,-150 978,-144 984,-144 984,-144 1085,-144 1085,-144 1091,-144 1097,-150 1097,-156 1097,-156 1097,-168 1097,-168 1097,-174 1091,-180 1085,-180"/>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1085,-180C1085,-180 984,-180 984,-180 978,-180 972,-174 972,-168 972,-168 972,-156 972,-156 972,-150 978,-144 984,-144 984,-144 1085,-144 1085,-144 1091,-144 1097,-150 1097,-156 1097,-156 1097,-168 1097,-168 1097,-174 1091,-180 1085,-180"/>
<text text-anchor="middle" x="1034.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
</g>
<!-- 32->10 -->
@@ -543,7 +543,7 @@
<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M313,-838C313,-838 12,-838 12,-838 6,-838 0,-832 0,-826 0,-826 0,-809 0,-809 0,-803 6,-797 12,-797 12,-797 313,-797 313,-797 319,-797 325,-803 325,-809 325,-809 325,-826 325,-826 325,-832 319,-838 313,-838"/>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M313,-838C313,-838 12,-838 12,-838 6,-838 0,-832 0,-826 0,-826 0,-809 0,-809 0,-803 6,-797 12,-797 12,-797 313,-797 313,-797 319,-797 325,-803 325,-809 325,-809 325,-826 325,-826 325,-832 319,-838 313,-838"/>
<text text-anchor="middle" x="162.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
<text text-anchor="middle" x="162.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
<text text-anchor="middle" x="162.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
@@ -557,7 +557,7 @@
<!-- 47 -->
<g id="node48" class="node">
<title>47</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M409,-761C409,-761 266,-761 266,-761 260,-761 254,-755 254,-749 254,-749 254,-737 254,-737 254,-731 260,-725 266,-725 266,-725 409,-725 409,-725 415,-725 421,-731 421,-737 421,-737 421,-749 421,-749 421,-755 415,-761 409,-761"/>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M409,-761C409,-761 266,-761 266,-761 260,-761 254,-755 254,-749 254,-749 254,-737 254,-737 254,-731 260,-725 266,-725 266,-725 409,-725 409,-725 415,-725 421,-731 421,-737 421,-737 421,-749 421,-749 421,-755 415,-761 409,-761"/>
<text text-anchor="middle" x="337.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
</g>
<!-- 33->47 -->
@@ -569,7 +569,7 @@
<!-- 34 -->
<g id="node35" class="node">
<title>34</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M676,-838C676,-838 363,-838 363,-838 357,-838 351,-832 351,-826 351,-826 351,-809 351,-809 351,-803 357,-797 363,-797 363,-797 676,-797 676,-797 682,-797 688,-803 688,-809 688,-809 688,-826 688,-826 688,-832 682,-838 676,-838"/>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M676,-838C676,-838 363,-838 363,-838 357,-838 351,-832 351,-826 351,-826 351,-809 351,-809 351,-803 357,-797 363,-797 363,-797 676,-797 676,-797 682,-797 688,-803 688,-809 688,-809 688,-826 688,-826 688,-832 682,-838 676,-838"/>
<text text-anchor="middle" x="519.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
<text text-anchor="middle" x="519.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
<text text-anchor="middle" x="519.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
@@ -583,7 +583,7 @@
<!-- 49 -->
<g id="node50" class="node">
<title>49</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M583.5,-761C583.5,-761 457.5,-761 457.5,-761 451.5,-761 445.5,-755 445.5,-749 445.5,-749 445.5,-737 445.5,-737 445.5,-731 451.5,-725 457.5,-725 457.5,-725 583.5,-725 583.5,-725 589.5,-725 595.5,-731 595.5,-737 595.5,-737 595.5,-749 595.5,-749 595.5,-755 589.5,-761 583.5,-761"/>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M583.5,-761C583.5,-761 457.5,-761 457.5,-761 451.5,-761 445.5,-755 445.5,-749 445.5,-749 445.5,-737 445.5,-737 445.5,-731 451.5,-725 457.5,-725 457.5,-725 583.5,-725 583.5,-725 589.5,-725 595.5,-731 595.5,-737 595.5,-737 595.5,-749 595.5,-749 595.5,-755 589.5,-761 583.5,-761"/>
<text text-anchor="middle" x="520.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
</g>
<!-- 34->49 -->
@@ -595,7 +595,7 @@
<!-- 35 -->
<g id="node36" class="node">
<title>35</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1070,-838C1070,-838 769,-838 769,-838 763,-838 757,-832 757,-826 757,-826 757,-809 757,-809 757,-803 763,-797 769,-797 769,-797 1070,-797 1070,-797 1076,-797 1082,-803 1082,-809 1082,-809 1082,-826 1082,-826 1082,-832 1076,-838 1070,-838"/>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1070,-838C1070,-838 769,-838 769,-838 763,-838 757,-832 757,-826 757,-826 757,-809 757,-809 757,-803 763,-797 769,-797 769,-797 1070,-797 1070,-797 1076,-797 1082,-803 1082,-809 1082,-809 1082,-826 1082,-826 1082,-832 1076,-838 1070,-838"/>
<text text-anchor="middle" x="919.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
<text text-anchor="middle" x="919.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq2</text>
<text text-anchor="middle" x="919.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
@@ -615,7 +615,7 @@
<!-- 36 -->
<g id="node37" class="node">
<title>36</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M401.5,-686.5C401.5,-686.5 273.5,-686.5 273.5,-686.5 267.5,-686.5 261.5,-680.5 261.5,-674.5 261.5,-674.5 261.5,-662.5 261.5,-662.5 261.5,-656.5 267.5,-650.5 273.5,-650.5 273.5,-650.5 401.5,-650.5 401.5,-650.5 407.5,-650.5 413.5,-656.5 413.5,-662.5 413.5,-662.5 413.5,-674.5 413.5,-674.5 413.5,-680.5 407.5,-686.5 401.5,-686.5"/>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M401.5,-686.5C401.5,-686.5 273.5,-686.5 273.5,-686.5 267.5,-686.5 261.5,-680.5 261.5,-674.5 261.5,-674.5 261.5,-662.5 261.5,-662.5 261.5,-656.5 267.5,-650.5 273.5,-650.5 273.5,-650.5 401.5,-650.5 401.5,-650.5 407.5,-650.5 413.5,-656.5 413.5,-662.5 413.5,-662.5 413.5,-674.5 413.5,-674.5 413.5,-680.5 407.5,-686.5 401.5,-686.5"/>
<text text-anchor="middle" x="337.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
<!-- 36->17 -->
@@ -639,7 +639,7 @@
<!-- 37 -->
<g id="node38" class="node">
<title>37</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M430,-324C430,-324 333,-324 333,-324 327,-324 321,-318 321,-312 321,-312 321,-300 321,-300 321,-294 327,-288 333,-288 333,-288 430,-288 430,-288 436,-288 442,-294 442,-300 442,-300 442,-312 442,-312 442,-318 436,-324 430,-324"/>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M430,-324C430,-324 333,-324 333,-324 327,-324 321,-318 321,-312 321,-312 321,-300 321,-300 321,-294 327,-288 333,-288 333,-288 430,-288 430,-288 436,-288 442,-294 442,-300 442,-300 442,-312 442,-312 442,-318 436,-324 430,-324"/>
<text text-anchor="middle" x="381.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
<!-- 37->17 -->
@@ -657,7 +657,7 @@
<!-- 38 -->
<g id="node39" class="node">
<title>38</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M577.5,-686.5C577.5,-686.5 467.5,-686.5 467.5,-686.5 461.5,-686.5 455.5,-680.5 455.5,-674.5 455.5,-674.5 455.5,-662.5 455.5,-662.5 455.5,-656.5 461.5,-650.5 467.5,-650.5 467.5,-650.5 577.5,-650.5 577.5,-650.5 583.5,-650.5 589.5,-656.5 589.5,-662.5 589.5,-662.5 589.5,-674.5 589.5,-674.5 589.5,-680.5 583.5,-686.5 577.5,-686.5"/>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M577.5,-686.5C577.5,-686.5 467.5,-686.5 467.5,-686.5 461.5,-686.5 455.5,-680.5 455.5,-674.5 455.5,-674.5 455.5,-662.5 455.5,-662.5 455.5,-656.5 461.5,-650.5 467.5,-650.5 467.5,-650.5 577.5,-650.5 577.5,-650.5 583.5,-650.5 589.5,-656.5 589.5,-662.5 589.5,-662.5 589.5,-674.5 589.5,-674.5 589.5,-680.5 583.5,-686.5 577.5,-686.5"/>
<text text-anchor="middle" x="522.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
<!-- 38->18 -->
@@ -681,7 +681,7 @@
<!-- 39 -->
<g id="node40" class="node">
<title>39</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M820,-396C820,-396 737,-396 737,-396 731,-396 725,-390 725,-384 725,-384 725,-372 725,-372 725,-366 731,-360 737,-360 737,-360 820,-360 820,-360 826,-360 832,-366 832,-372 832,-372 832,-384 832,-384 832,-390 826,-396 820,-396"/>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M820,-396C820,-396 737,-396 737,-396 731,-396 725,-390 725,-384 725,-384 725,-372 725,-372 725,-366 731,-360 737,-360 737,-360 820,-360 820,-360 826,-360 832,-366 832,-372 832,-372 832,-384 832,-384 832,-390 826,-396 820,-396"/>
<text text-anchor="middle" x="778.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
</g>
<!-- 39->19 -->
@@ -693,7 +693,7 @@
<!-- 40 -->
<g id="node41" class="node">
<title>40</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1260.5,-252C1260.5,-252 1168.5,-252 1168.5,-252 1162.5,-252 1156.5,-246 1156.5,-240 1156.5,-240 1156.5,-228 1156.5,-228 1156.5,-222 1162.5,-216 1168.5,-216 1168.5,-216 1260.5,-216 1260.5,-216 1266.5,-216 1272.5,-222 1272.5,-228 1272.5,-228 1272.5,-240 1272.5,-240 1272.5,-246 1266.5,-252 1260.5,-252"/>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M1260.5,-252C1260.5,-252 1168.5,-252 1168.5,-252 1162.5,-252 1156.5,-246 1156.5,-240 1156.5,-240 1156.5,-228 1156.5,-228 1156.5,-222 1162.5,-216 1168.5,-216 1168.5,-216 1260.5,-216 1260.5,-216 1266.5,-216 1272.5,-222 1272.5,-228 1272.5,-228 1272.5,-240 1272.5,-240 1272.5,-246 1266.5,-252 1260.5,-252"/>
<text text-anchor="middle" x="1214.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
</g>
<!-- 40->20 -->
@@ -705,7 +705,7 @@
<!-- 41 -->
<g id="node42" class="node">
<title>41</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1394.5,-252C1394.5,-252 1302.5,-252 1302.5,-252 1296.5,-252 1290.5,-246 1290.5,-240 1290.5,-240 1290.5,-228 1290.5,-228 1290.5,-222 1296.5,-216 1302.5,-216 1302.5,-216 1394.5,-216 1394.5,-216 1400.5,-216 1406.5,-222 1406.5,-228 1406.5,-228 1406.5,-240 1406.5,-240 1406.5,-246 1400.5,-252 1394.5,-252"/>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M1394.5,-252C1394.5,-252 1302.5,-252 1302.5,-252 1296.5,-252 1290.5,-246 1290.5,-240 1290.5,-240 1290.5,-228 1290.5,-228 1290.5,-222 1296.5,-216 1302.5,-216 1302.5,-216 1394.5,-216 1394.5,-216 1400.5,-216 1406.5,-222 1406.5,-228 1406.5,-228 1406.5,-240 1406.5,-240 1406.5,-246 1400.5,-252 1394.5,-252"/>
<text text-anchor="middle" x="1348.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
</g>
<!-- 41->20 -->
@@ -717,7 +717,7 @@
<!-- 42 -->
<g id="node43" class="node">
<title>42</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1022.5,-396C1022.5,-396 900.5,-396 900.5,-396 894.5,-396 888.5,-390 888.5,-384 888.5,-384 888.5,-372 888.5,-372 888.5,-366 894.5,-360 900.5,-360 900.5,-360 1022.5,-360 1022.5,-360 1028.5,-360 1034.5,-366 1034.5,-372 1034.5,-372 1034.5,-384 1034.5,-384 1034.5,-390 1028.5,-396 1022.5,-396"/>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1022.5,-396C1022.5,-396 900.5,-396 900.5,-396 894.5,-396 888.5,-390 888.5,-384 888.5,-384 888.5,-372 888.5,-372 888.5,-366 894.5,-360 900.5,-360 900.5,-360 1022.5,-360 1022.5,-360 1028.5,-360 1034.5,-366 1034.5,-372 1034.5,-372 1034.5,-384 1034.5,-384 1034.5,-390 1028.5,-396 1022.5,-396"/>
<text text-anchor="middle" x="961.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
<text text-anchor="middle" x="961.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
</g>
@@ -736,7 +736,7 @@
<!-- 52 -->
<g id="node53" class="node">
<title>52</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M998.5,-324C998.5,-324 968.5,-324 968.5,-324 962.5,-324 956.5,-318 956.5,-312 956.5,-312 956.5,-300 956.5,-300 956.5,-294 962.5,-288 968.5,-288 968.5,-288 998.5,-288 998.5,-288 1004.5,-288 1010.5,-294 1010.5,-300 1010.5,-300 1010.5,-312 1010.5,-312 1010.5,-318 1004.5,-324 998.5,-324"/>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M998.5,-324C998.5,-324 968.5,-324 968.5,-324 962.5,-324 956.5,-318 956.5,-312 956.5,-312 956.5,-300 956.5,-300 956.5,-294 962.5,-288 968.5,-288 968.5,-288 998.5,-288 998.5,-288 1004.5,-288 1010.5,-294 1010.5,-300 1010.5,-300 1010.5,-312 1010.5,-312 1010.5,-318 1004.5,-324 998.5,-324"/>
<text text-anchor="middle" x="983.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
<!-- 42->52 -->
@@ -748,7 +748,7 @@
<!-- 43 -->
<g id="node44" class="node">
<title>43</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1186.5,-396C1186.5,-396 1064.5,-396 1064.5,-396 1058.5,-396 1052.5,-390 1052.5,-384 1052.5,-384 1052.5,-372 1052.5,-372 1052.5,-366 1058.5,-360 1064.5,-360 1064.5,-360 1186.5,-360 1186.5,-360 1192.5,-360 1198.5,-366 1198.5,-372 1198.5,-372 1198.5,-384 1198.5,-384 1198.5,-390 1192.5,-396 1186.5,-396"/>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1186.5,-396C1186.5,-396 1064.5,-396 1064.5,-396 1058.5,-396 1052.5,-390 1052.5,-384 1052.5,-384 1052.5,-372 1052.5,-372 1052.5,-366 1058.5,-360 1064.5,-360 1064.5,-360 1186.5,-360 1186.5,-360 1192.5,-360 1198.5,-366 1198.5,-372 1198.5,-372 1198.5,-384 1198.5,-384 1198.5,-390 1192.5,-396 1186.5,-396"/>
<text text-anchor="middle" x="1125.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
<text text-anchor="middle" x="1125.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
</g>
@@ -767,7 +767,7 @@
<!-- 54 -->
<g id="node55" class="node">
<title>54</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1286.5,-324C1286.5,-324 1256.5,-324 1256.5,-324 1250.5,-324 1244.5,-318 1244.5,-312 1244.5,-312 1244.5,-300 1244.5,-300 1244.5,-294 1250.5,-288 1256.5,-288 1256.5,-288 1286.5,-288 1286.5,-288 1292.5,-288 1298.5,-294 1298.5,-300 1298.5,-300 1298.5,-312 1298.5,-312 1298.5,-318 1292.5,-324 1286.5,-324"/>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1286.5,-324C1286.5,-324 1256.5,-324 1256.5,-324 1250.5,-324 1244.5,-318 1244.5,-312 1244.5,-312 1244.5,-300 1244.5,-300 1244.5,-294 1250.5,-288 1256.5,-288 1256.5,-288 1286.5,-288 1286.5,-288 1292.5,-288 1298.5,-294 1298.5,-300 1298.5,-300 1298.5,-312 1298.5,-312 1298.5,-318 1292.5,-324 1286.5,-324"/>
<text text-anchor="middle" x="1271.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
<!-- 43->54 -->
@@ -779,7 +779,7 @@
<!-- 44 -->
<g id="node45" class="node">
<title>44</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1891.5,-396C1891.5,-396 1769.5,-396 1769.5,-396 1763.5,-396 1757.5,-390 1757.5,-384 1757.5,-384 1757.5,-372 1757.5,-372 1757.5,-366 1763.5,-360 1769.5,-360 1769.5,-360 1891.5,-360 1891.5,-360 1897.5,-360 1903.5,-366 1903.5,-372 1903.5,-372 1903.5,-384 1903.5,-384 1903.5,-390 1897.5,-396 1891.5,-396"/>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1891.5,-396C1891.5,-396 1769.5,-396 1769.5,-396 1763.5,-396 1757.5,-390 1757.5,-384 1757.5,-384 1757.5,-372 1757.5,-372 1757.5,-366 1763.5,-360 1769.5,-360 1769.5,-360 1891.5,-360 1891.5,-360 1897.5,-360 1903.5,-366 1903.5,-372 1903.5,-372 1903.5,-384 1903.5,-384 1903.5,-390 1897.5,-396 1891.5,-396"/>
<text text-anchor="middle" x="1830.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
<text text-anchor="middle" x="1830.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
</g>
@@ -798,7 +798,7 @@
<!-- 53 -->
<g id="node54" class="node">
<title>53</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1542.5,-324C1542.5,-324 1512.5,-324 1512.5,-324 1506.5,-324 1500.5,-318 1500.5,-312 1500.5,-312 1500.5,-300 1500.5,-300 1500.5,-294 1506.5,-288 1512.5,-288 1512.5,-288 1542.5,-288 1542.5,-288 1548.5,-288 1554.5,-294 1554.5,-300 1554.5,-300 1554.5,-312 1554.5,-312 1554.5,-318 1548.5,-324 1542.5,-324"/>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1542.5,-324C1542.5,-324 1512.5,-324 1512.5,-324 1506.5,-324 1500.5,-318 1500.5,-312 1500.5,-312 1500.5,-300 1500.5,-300 1500.5,-294 1506.5,-288 1512.5,-288 1512.5,-288 1542.5,-288 1542.5,-288 1548.5,-288 1554.5,-294 1554.5,-300 1554.5,-300 1554.5,-312 1554.5,-312 1554.5,-318 1548.5,-324 1542.5,-324"/>
<text text-anchor="middle" x="1527.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
<!-- 44->53 -->
@@ -810,7 +810,7 @@
<!-- 45 -->
<g id="node46" class="node">
<title>45</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M2055.5,-396C2055.5,-396 1933.5,-396 1933.5,-396 1927.5,-396 1921.5,-390 1921.5,-384 1921.5,-384 1921.5,-372 1921.5,-372 1921.5,-366 1927.5,-360 1933.5,-360 1933.5,-360 2055.5,-360 2055.5,-360 2061.5,-360 2067.5,-366 2067.5,-372 2067.5,-372 2067.5,-384 2067.5,-384 2067.5,-390 2061.5,-396 2055.5,-396"/>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M2055.5,-396C2055.5,-396 1933.5,-396 1933.5,-396 1927.5,-396 1921.5,-390 1921.5,-384 1921.5,-384 1921.5,-372 1921.5,-372 1921.5,-366 1927.5,-360 1933.5,-360 1933.5,-360 2055.5,-360 2055.5,-360 2061.5,-360 2067.5,-366 2067.5,-372 2067.5,-372 2067.5,-384 2067.5,-384 2067.5,-390 2061.5,-396 2055.5,-396"/>
<text text-anchor="middle" x="1994.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
<text text-anchor="middle" x="1994.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
</g>
@@ -829,7 +829,7 @@
<!-- 55 -->
<g id="node56" class="node">
<title>55</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1614.5,-324C1614.5,-324 1584.5,-324 1584.5,-324 1578.5,-324 1572.5,-318 1572.5,-312 1572.5,-312 1572.5,-300 1572.5,-300 1572.5,-294 1578.5,-288 1584.5,-288 1584.5,-288 1614.5,-288 1614.5,-288 1620.5,-288 1626.5,-294 1626.5,-300 1626.5,-300 1626.5,-312 1626.5,-312 1626.5,-318 1620.5,-324 1614.5,-324"/>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1614.5,-324C1614.5,-324 1584.5,-324 1584.5,-324 1578.5,-324 1572.5,-318 1572.5,-312 1572.5,-312 1572.5,-300 1572.5,-300 1572.5,-294 1578.5,-288 1584.5,-288 1584.5,-288 1614.5,-288 1614.5,-288 1620.5,-288 1626.5,-294 1626.5,-300 1626.5,-300 1626.5,-312 1626.5,-312 1626.5,-318 1620.5,-324 1614.5,-324"/>
<text text-anchor="middle" x="1599.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
<!-- 45->55 -->
@@ -859,7 +859,7 @@
<!-- 48 -->
<g id="node49" class="node">
<title>48</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M448,-396C448,-396 333,-396 333,-396 327,-396 321,-390 321,-384 321,-384 321,-372 321,-372 321,-366 327,-360 333,-360 333,-360 448,-360 448,-360 454,-360 460,-366 460,-372 460,-372 460,-384 460,-384 460,-390 454,-396 448,-396"/>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M448,-396C448,-396 333,-396 333,-396 327,-396 321,-390 321,-384 321,-384 321,-372 321,-372 321,-366 327,-360 333,-360 333,-360 448,-360 448,-360 454,-360 460,-366 460,-372 460,-372 460,-384 460,-384 460,-390 454,-396 448,-396"/>
<text text-anchor="middle" x="390.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
<text text-anchor="middle" x="390.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
</g>
@@ -890,7 +890,7 @@
<!-- 50 -->
<g id="node51" class="node">
<title>50</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M859,-468C859,-468 764,-468 764,-468 758,-468 752,-462 752,-456 752,-456 752,-444 752,-444 752,-438 758,-432 764,-432 764,-432 859,-432 859,-432 865,-432 871,-438 871,-444 871,-444 871,-456 871,-456 871,-462 865,-468 859,-468"/>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M859,-468C859,-468 764,-468 764,-468 758,-468 752,-462 752,-456 752,-456 752,-444 752,-444 752,-438 758,-432 764,-432 764,-432 859,-432 859,-432 865,-432 871,-438 871,-444 871,-444 871,-456 871,-456 871,-462 865,-468 859,-468"/>
<text text-anchor="middle" x="811.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 50->39 -->
@@ -902,7 +902,7 @@
<!-- 51 -->
<g id="node52" class="node">
<title>51</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M1015,-468C1015,-468 920,-468 920,-468 914,-468 908,-462 908,-456 908,-456 908,-444 908,-444 908,-438 914,-432 920,-432 920,-432 1015,-432 1015,-432 1021,-432 1027,-438 1027,-444 1027,-444 1027,-456 1027,-456 1027,-462 1021,-468 1015,-468"/>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1015,-468C1015,-468 920,-468 920,-468 914,-468 908,-462 908,-456 908,-456 908,-444 908,-444 908,-438 914,-432 920,-432 920,-432 1015,-432 1015,-432 1021,-432 1027,-438 1027,-444 1027,-444 1027,-456 1027,-456 1027,-462 1021,-468 1015,-468"/>
<text text-anchor="middle" x="967.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 51->39 -->
@@ -938,7 +938,7 @@
<!-- 56 -->
<g id="node57" class="node">
<title>56</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M712.5,-468C712.5,-468 676.5,-468 676.5,-468 670.5,-468 664.5,-462 664.5,-456 664.5,-456 664.5,-444 664.5,-444 664.5,-438 670.5,-432 676.5,-432 676.5,-432 712.5,-432 712.5,-432 718.5,-432 724.5,-438 724.5,-444 724.5,-444 724.5,-456 724.5,-456 724.5,-462 718.5,-468 712.5,-468"/>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M712.5,-468C712.5,-468 676.5,-468 676.5,-468 670.5,-468 664.5,-462 664.5,-456 664.5,-456 664.5,-444 664.5,-444 664.5,-438 670.5,-432 676.5,-432 676.5,-432 712.5,-432 712.5,-432 718.5,-432 724.5,-438 724.5,-444 724.5,-444 724.5,-456 724.5,-456 724.5,-462 718.5,-468 712.5,-468"/>
<text text-anchor="middle" x="694.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
</g>
<!-- 56->42 -->
@@ -956,7 +956,7 @@
<!-- 57 -->
<g id="node58" class="node">
<title>57</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M1827.5,-468C1827.5,-468 1791.5,-468 1791.5,-468 1785.5,-468 1779.5,-462 1779.5,-456 1779.5,-456 1779.5,-444 1779.5,-444 1779.5,-438 1785.5,-432 1791.5,-432 1791.5,-432 1827.5,-432 1827.5,-432 1833.5,-432 1839.5,-438 1839.5,-444 1839.5,-444 1839.5,-456 1839.5,-456 1839.5,-462 1833.5,-468 1827.5,-468"/>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1827.5,-468C1827.5,-468 1791.5,-468 1791.5,-468 1785.5,-468 1779.5,-462 1779.5,-456 1779.5,-456 1779.5,-444 1779.5,-444 1779.5,-438 1785.5,-432 1791.5,-432 1791.5,-432 1827.5,-432 1827.5,-432 1833.5,-432 1839.5,-438 1839.5,-444 1839.5,-444 1839.5,-456 1839.5,-456 1839.5,-462 1833.5,-468 1827.5,-468"/>
<text text-anchor="middle" x="1809.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
</g>
<!-- 57->44 -->
@@ -992,7 +992,7 @@
<!-- 60 -->
<g id="node61" class="node">
<title>60</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M776.5,-540C776.5,-540 604.5,-540 604.5,-540 598.5,-540 592.5,-534 592.5,-528 592.5,-528 592.5,-516 592.5,-516 592.5,-510 598.5,-504 604.5,-504 604.5,-504 776.5,-504 776.5,-504 782.5,-504 788.5,-510 788.5,-516 788.5,-516 788.5,-528 788.5,-528 788.5,-534 782.5,-540 776.5,-540"/>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M776.5,-540C776.5,-540 604.5,-540 604.5,-540 598.5,-540 592.5,-534 592.5,-528 592.5,-528 592.5,-516 592.5,-516 592.5,-510 598.5,-504 604.5,-504 604.5,-504 776.5,-504 776.5,-504 782.5,-504 788.5,-510 788.5,-516 788.5,-516 788.5,-528 788.5,-528 788.5,-534 782.5,-540 776.5,-540"/>
<text text-anchor="middle" x="690.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="690.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">seqmode: pe</text>
</g>
@@ -1017,7 +1017,7 @@
<!-- 61 -->
<g id="node62" class="node">
<title>61</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M992.5,-540C992.5,-540 856.5,-540 856.5,-540 850.5,-540 844.5,-534 844.5,-528 844.5,-528 844.5,-516 844.5,-516 844.5,-510 850.5,-504 856.5,-504 856.5,-504 992.5,-504 992.5,-504 998.5,-504 1004.5,-510 1004.5,-516 1004.5,-516 1004.5,-528 1004.5,-528 1004.5,-534 998.5,-540 992.5,-540"/>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M992.5,-540C992.5,-540 856.5,-540 856.5,-540 850.5,-540 844.5,-534 844.5,-528 844.5,-528 844.5,-516 844.5,-516 844.5,-510 850.5,-504 856.5,-504 856.5,-504 992.5,-504 992.5,-504 998.5,-504 1004.5,-510 1004.5,-516 1004.5,-516 1004.5,-528 1004.5,-528 1004.5,-534 998.5,-540 992.5,-540"/>
<text text-anchor="middle" x="924.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
<!-- 61->50 -->
@@ -1047,7 +1047,7 @@
<!-- 63 -->
<g id="node64" class="node">
<title>63</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1282.5,-540C1282.5,-540 1110.5,-540 1110.5,-540 1104.5,-540 1098.5,-534 1098.5,-528 1098.5,-528 1098.5,-516 1098.5,-516 1098.5,-510 1104.5,-504 1110.5,-504 1110.5,-504 1282.5,-504 1282.5,-504 1288.5,-504 1294.5,-510 1294.5,-516 1294.5,-516 1294.5,-528 1294.5,-528 1294.5,-534 1288.5,-540 1282.5,-540"/>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1282.5,-540C1282.5,-540 1110.5,-540 1110.5,-540 1104.5,-540 1098.5,-534 1098.5,-528 1098.5,-528 1098.5,-516 1098.5,-516 1098.5,-510 1104.5,-504 1110.5,-504 1110.5,-504 1282.5,-504 1282.5,-504 1288.5,-504 1294.5,-510 1294.5,-516 1294.5,-516 1294.5,-528 1294.5,-528 1294.5,-534 1288.5,-540 1282.5,-540"/>
<text text-anchor="middle" x="1196.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="1196.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">seqmode: se</text>
</g>
diff --git a/scripts/prepare_inputs.dict.tsv b/scripts/prepare_inputs.dict.tsv
index 0a54bf6..ab2f741 100644
--- a/scripts/prepare_inputs.dict.tsv
+++ b/scripts/prepare_inputs.dict.tsv
@@ -2,7 +2,7 @@ labkey snakemake
Entry_Date entry_date
Path_Fastq_Files fastq_path
Condition_Name condition
-Replicate_Name replicate_name
+Sample_Name sample_name
Single_Paired seqmode
Mate1_File fq1
Mate2_File fq2
diff --git a/scripts/prepare_inputs.py b/scripts/prepare_inputs.py
index 5bcfb9b..426902a 100755
--- a/scripts/prepare_inputs.py
+++ b/scripts/prepare_inputs.py
@@ -512,7 +512,7 @@ def main(args):
for index, row in input_table.iterrows():
# extract data from LabKey-like table
- lk_replicate_name = row[input_dict.loc['replicate_name', 'labkey']]
+ lk_sample_name = row[input_dict.loc['sample_name', 'labkey']]
lk_condition = row[input_dict.loc['condition', 'labkey']]
lk_seqmode = row[input_dict.loc['seqmode', 'labkey']]
lk_fastq_path = row[input_dict.loc['fastq_path', 'labkey']]
@@ -539,7 +539,7 @@ def main(args):
)
else:
anchor = os.path.abspath(os.path.dirname(args.table))
- sample = "_".join([lk_replicate_name, lk_condition])
+ sample = "_".join([lk_sample_name, lk_condition])
if lk_seqmode == 'PAIRED':
seqmode = 'pe'
fq2 = expand_path(
diff --git a/tests/input_files/pe_lane1/synthetic_split_lane1.mate_1.fastq.gz b/tests/input_files/pe_lane1/synthetic_split_lane1.mate_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..271cc8cef1d054f2737245901609b6d927b4e157
GIT binary patch
literal 445
zcmb2|=HU1yaxsp9xwtZ~BqOyXGdVsdF)!6nFE_CyHQrD!EwQ+ykfC?-*}Ovr0xj<=
zyS!|R3V053PUQE|&DIWm6eNG^d;P?7YZ$k(d-!hp7b*Pqx#WEP`Ns=wj-<w3O04~V
zufAsg&G5*_Qpqxs%T0{?GV3~Dr^<#iM`>Rx3-i+E&DD@O@Zd93z1KsTUgx}LdVI4!
z<y@<YNH~>Yy+7km!>7Y}90}E~wYL`72u)yi=6&Ghr}%V9!<kHvM2q|bZ<oI;5W4e8
zz;CM%ug(N#CNpFGT@(4wojP^3b4_}n&*o<y%Zf9s<PIHt7*Vx+#s1w<&JQLtbN=|W
z+%PL%c;@zdPjh!z%)Jy?u>AO`ol-$(z0>_vH-{BxX_voU^Z)pkSDd*ovdS!F^(^kR
z6-h4eV>!hqXOx$*Bvj$UwxYtAN5vMhJE!ZdJ@fY2(O*XlTN1)Qa|zBBK9pr8{4jf|
zw)ngQ7n?)*mXukldnmMdDep>BQ85$$T%RL3y<!%pc|ZTdbxkK5_t+XKKbU^X%18a%
z>D0WV^Ik`n=!(vs{cFAMZpp)E7jl$$3pp)QQJC6%W|pjPL97L*#UBQ(t7XxFEDQ_)
D0D#IV
literal 0
HcmV?d00001
diff --git a/tests/input_files/pe_lane1/synthetic_split_lane1.mate_2.fastq.gz b/tests/input_files/pe_lane1/synthetic_split_lane1.mate_2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..98edea4069db6cc2e12d958da2877b1fe7947854
GIT binary patch
literal 442
zcmb2|=HPG>yBNp7TwIw~l95`HnH-;!n3rm(mz!9U8gHbRmRMX;$k03aY~CRQftL4`
zU0$|D1w03TPUQDldt$0q;Y+zwzxR8jUu(GKJgd!M<8`%L{gUzP=0D$Oe>8LErOe9x
zvi5oTUsvlCb{c-WqS$-Iu2=u~(_LS@S<iTFb=E!Fb<iqg^&ajlL($cRCvvBr(&YO7
zn~y;%L!C?ggW~HbL*8A^;#)p+eLc?|<<3;JU=8D%Cn7<9LMeXETz6C1-&yc1k1V)s
zHfLAL<(7o{RbpB$ias;^H3aHK_gwxh_E+}bgV|jV9u(y44P0X{|5}Ray^O~JeS4|o
zT+@j^ugX=*>+uy^ap&D@F?QVGwD#R3pX@zf{S=e$M7=GUEc^ZCY-zv39S;hu&!sll
z32InZoTykZG0f>f?eir2qp}uaH{_QdkegW?oihD-@I;;7396HS^t-;9_j~udf+e@x
zlG(ylC)|5FN1<6myZJ@m#0fWap8Y>!<X0%iY5r|?!IxuK*89z#Y3?bq-B<74`9$O8
zQJ+259PL+%>ZuK@JHDya&_<~1Lyv}{h!@i(ON})*FS1<kncR5SJov#U%Rm+e1^~1l
B&Dj6|
literal 0
HcmV?d00001
diff --git a/tests/input_files/pe_lane2/synthetic_split_lane2.mate_1.fastq.gz b/tests/input_files/pe_lane2/synthetic_split_lane2.mate_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..6ec3e5ddd52038029d50a21088ab8706cc6512cf
GIT binary patch
literal 415
zcmb2|=HLhyy%@*9TwIw~l95`HnH-;!n3rm#mz!9U8gHnVmRMX;$gp(s*{s6`0xj?B
zx}5qgPjty16}3v)JwsQdXeHm--}^n%!~Eu6SfW|d`!6l^!tzMjKKb4I<R490Zt`UN
z<!^t#WX+$I+-LaBuwS#!^4sqpBA*Sv-*m|eT`e8FHfm{E$dXx!E16cVT9MevtCiN&
z7+DhW=yS^^@$;X}UuY%WT_$|&v(Aq^*Mun{DoX@ZwjA?V8IW`>T63wjO~UMBThwnC
zoK4e~c6)g6M0#7L=$gu+wikz#suX{@h6qS@%#E=q-sWP)@}TKV??*0?<Hy!1om8F@
z*^+ZlMt|$K3A%pzE7fCm<;Pg7rF^=YCf}GT8l2n29r(^s>Rw<--gMUz)`Ek*lQ$Qe
zzn#o9`+;0#i}{4K%mf#a@1}nk^?Y~#u#PTn{MstB?*6LJ25U{8z2VuOe2yvR$K1=8
zpFP+m_SF2CtL3_L4?l2}#C7<zZVF3@@cO>7@Nr$ij+c6K=EYzBKmQ*8j@#$^tTOJb
aessn~_w1fSS<B|_($7$+o9oBIzyJVz`N>rP
literal 0
HcmV?d00001
diff --git a/tests/input_files/pe_lane2/synthetic_split_lane2.mate_2.fastq.gz b/tests/input_files/pe_lane2/synthetic_split_lane2.mate_2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..693389493c4dc5a9a843b853783beb05ea0b37b5
GIT binary patch
literal 407
zcmb2|=HSQ_yBNp7TwIw~l95`HnH-;!n3rm#mz!9U8gHbRmRMX;$gp(s!K}juJZ<kQ
zyAJl*TI2<p8r%5@J2pG&Urwz3FFvzwXJpigTL-Ub&4@R9@mXK~SKW!=nHd`IpZ`7n
z(|7-pCzFcb6-#RNtA0QJXN&&wOX8_!!dvHd&5(#*{>nSBQR`5bKxi?m=CV_92H^|b
zuR0xnR;Ki7)!lW;M?RnVce|@)MTljf*PJM&4lR`s<?OY0U%&iZ(4Q;yl4IM$X};lR
zoI;mhT%7z^x}c};;@<T&=8HAFzkZ6(a}qaWn%#a_b)NKN-WA*5?$!!+S!HZ|Ly5UR
z$}Z*fW$v#Hi>;4UUKiiL=fy5FeaW^Mm*j^Jjz{jkcXL~zj*MPw;U0_aneyS=Pu^wb
zf6SKgjE&8OFaEOpgAA)DzjNBw8795(Tl7)F{bGi_!t9=xUwVq)I*G+6t_i=k@Xx^=
zQpc}a=HEMPZ`h%+beCVsuAX<vkB>bTD7d`7;D3FFkpDHa2ixY$mMrI7pJl+j)$Fs@
SGD)k_`>VP+R(Z29FaQ9>jKsqL
literal 0
HcmV?d00001
diff --git a/tests/input_files/samples_concat.tsv b/tests/input_files/samples_concat.tsv
new file mode 100644
index 0000000..6740f70
--- /dev/null
+++ b/tests/input_files/samples_concat.tsv
@@ -0,0 +1,7 @@
+sample seqmode fq1 fq2 index_size kmer fq1_3p fq1_5p fq2_3p fq2_5p organism gtf genome sd mean kallisto_directionality alfa_directionality alfa_plus alfa_minus multimappers soft_clip pass_mode libtype fq1_polya_3p fq1_polya_5p fq2_polya_3p fq2_polya_5p
+synthetic_split_10_reads_paired_synthetic_split_10_reads_paired pe ../input_files/pe_lane1/synthetic_split_lane1.mate_1.fastq.gz ../input_files/pe_lane1/synthetic_split_lane1.mate_2.fastq.gz 74 31 AGATCGGAAGAGCACA XXXXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 --fr fr-firststrand str1 str2 10 EndToEnd None A AAAAAAAAAAAAAAA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX TTTTTTTTTTTTTTT
+synthetic_split_10_reads_paired_synthetic_split_10_reads_paired pe ../input_files/pe_lane2/synthetic_split_lane2.mate_1.fastq.gz ../input_files/pe_lane2/synthetic_split_lane2.mate_2.fastq.gz 74 31 AGATCGGAAGAGCACA XXXXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 --fr fr-firststrand str1 str2 10 EndToEnd None A AAAAAAAAAAAAAAA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX TTTTTTTTTTTTTTT
+synthetic_10_reads_paired_synthetic_10_reads_paired pe ../input_files/project1/synthetic.mate_1.fastq.gz ../input_files/project1/synthetic.mate_2.fastq.gz 74 31 AGATCGGAAGAGCACA XXXXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 --fr fr-firststrand str1 str2 10 EndToEnd None A AAAAAAAAAAAAAAA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX TTTTTTTTTTTTTTT
+synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 se ../input_files/project2/synthetic.mate_1.fastq.gz XXXXXXXXXXXXXXX 74 31 AGATCGGAAGAGCACA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 --fr fr-firststrand str1 str2 10 EndToEnd None A AAAAAAAAAAAAAAA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX
+synthetic_split_10_reads_mate_1_synthetic_split_10_reads_mate_1 se ../input_files/se_lane1/synthetic_split_lane1.mate_1.fastq.gz XXXXXXXXXXXXXXX 74 31 AGATCGGAAGAGCACA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 --fr fr-firststrand str1 str2 10 EndToEnd None A AAAAAAAAAAAAAAA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX
+synthetic_split_10_reads_mate_1_synthetic_split_10_reads_mate_1 se ../input_files/se_lane2/synthetic_split_lane2.mate_1.fastq.gz XXXXXXXXXXXXXXX 74 31 AGATCGGAAGAGCACA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 --fr fr-firststrand str1 str2 10 EndToEnd None A AAAAAAAAAAAAAAA XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX XXXXXXXXXXXXXXX
diff --git a/tests/input_files/se_lane1/synthetic_split_lane1.mate_1.fastq.gz b/tests/input_files/se_lane1/synthetic_split_lane1.mate_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..271cc8cef1d054f2737245901609b6d927b4e157
GIT binary patch
literal 445
zcmb2|=HU1yaxsp9xwtZ~BqOyXGdVsdF)!6nFE_CyHQrD!EwQ+ykfC?-*}Ovr0xj<=
zyS!|R3V053PUQE|&DIWm6eNG^d;P?7YZ$k(d-!hp7b*Pqx#WEP`Ns=wj-<w3O04~V
zufAsg&G5*_Qpqxs%T0{?GV3~Dr^<#iM`>Rx3-i+E&DD@O@Zd93z1KsTUgx}LdVI4!
z<y@<YNH~>Yy+7km!>7Y}90}E~wYL`72u)yi=6&Ghr}%V9!<kHvM2q|bZ<oI;5W4e8
zz;CM%ug(N#CNpFGT@(4wojP^3b4_}n&*o<y%Zf9s<PIHt7*Vx+#s1w<&JQLtbN=|W
z+%PL%c;@zdPjh!z%)Jy?u>AO`ol-$(z0>_vH-{BxX_voU^Z)pkSDd*ovdS!F^(^kR
z6-h4eV>!hqXOx$*Bvj$UwxYtAN5vMhJE!ZdJ@fY2(O*XlTN1)Qa|zBBK9pr8{4jf|
zw)ngQ7n?)*mXukldnmMdDep>BQ85$$T%RL3y<!%pc|ZTdbxkK5_t+XKKbU^X%18a%
z>D0WV^Ik`n=!(vs{cFAMZpp)E7jl$$3pp)QQJC6%W|pjPL97L*#UBQ(t7XxFEDQ_)
D0D#IV
literal 0
HcmV?d00001
diff --git a/tests/input_files/se_lane2/synthetic_split_lane2.mate_1.fastq.gz b/tests/input_files/se_lane2/synthetic_split_lane2.mate_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..6ec3e5ddd52038029d50a21088ab8706cc6512cf
GIT binary patch
literal 415
zcmb2|=HLhyy%@*9TwIw~l95`HnH-;!n3rm#mz!9U8gHnVmRMX;$gp(s*{s6`0xj?B
zx}5qgPjty16}3v)JwsQdXeHm--}^n%!~Eu6SfW|d`!6l^!tzMjKKb4I<R490Zt`UN
z<!^t#WX+$I+-LaBuwS#!^4sqpBA*Sv-*m|eT`e8FHfm{E$dXx!E16cVT9MevtCiN&
z7+DhW=yS^^@$;X}UuY%WT_$|&v(Aq^*Mun{DoX@ZwjA?V8IW`>T63wjO~UMBThwnC
zoK4e~c6)g6M0#7L=$gu+wikz#suX{@h6qS@%#E=q-sWP)@}TKV??*0?<Hy!1om8F@
z*^+ZlMt|$K3A%pzE7fCm<;Pg7rF^=YCf}GT8l2n29r(^s>Rw<--gMUz)`Ek*lQ$Qe
zzn#o9`+;0#i}{4K%mf#a@1}nk^?Y~#u#PTn{MstB?*6LJ25U{8z2VuOe2yvR$K1=8
zpFP+m_SF2CtL3_L4?l2}#C7<zZVF3@@cO>7@Nr$ij+c6K=EYzBKmQ*8j@#$^tTOJb
aessn~_w1fSS<B|_($7$+o9oBIzyJVz`N>rP
literal 0
HcmV?d00001
diff --git a/tests/test_scripts_prepare_inputs_labkey/test.sh b/tests/test_scripts_prepare_inputs_labkey/test.sh
index 3f8b721..dea4515 100755
--- a/tests/test_scripts_prepare_inputs_labkey/test.sh
+++ b/tests/test_scripts_prepare_inputs_labkey/test.sh
@@ -40,7 +40,7 @@ python "../../scripts/prepare_inputs.py" \
--multimappers='10' \
--logo="../../images/logo.128px.png" \
--debug \
- "RNA_Seq_data_template"
+ "RNA_Seq_data_template_raw"
# Check if dry run completes
snakemake \
diff --git a/tests/test_scripts_prepare_inputs_table/input_table.tsv b/tests/test_scripts_prepare_inputs_table/input_table.tsv
index ee6d5fc..10b0244 100644
--- a/tests/test_scripts_prepare_inputs_table/input_table.tsv
+++ b/tests/test_scripts_prepare_inputs_table/input_table.tsv
@@ -1,3 +1,3 @@
-Mate2_5p_Adapter Condition_Name Name_Quality_Control_File_Mate1 Disease_Short_Name Single_Paired Gender Entry_Date Disease_Description Strain_Isolate_Breed_Ecotype Genotype_Description Mate1_File Source_Tissue_Name Developmental_Stage Mate1_Direction Quality_Control_Flag Genotype_Short_Name Strain_Isolate_Breed_Ecotype_ID Fragment_Length_Mean Organism Contaminant_Sequences TaxonID Documentation Prepared_By _labkeyurl_Entry_Date Molecule Mate2_Direction Library_preparation_kit Checksum_Raw_FASTQ_Mate1 Cycles Fragment_Length_SD Replicate_Name Passage_Number Mate1_5p_Adapter Mate2_3p_Adapter Path_Fastq_Files Mate1_3p_Adapter Treatment_Short_Name Age Sequencing_Date Checksum_Raw_FASTQ_Mate2 Biomaterial_Provider Treatment_Description Sample_Preparation_Date BioAnalyzer_File Sequencing_Instrument Additional_Tissue_Description Protocol_File Name_Quality_Control_File_Mate2 Tissue_Code File_Name_Metadata_File Mate2_File
+Mate2_5p_Adapter Condition_Name Name_Quality_Control_File_Mate1 Disease_Short_Name Single_Paired Gender Entry_Date Disease_Description Strain_Isolate_Breed_Ecotype Genotype_Description Mate1_File Source_Tissue_Name Developmental_Stage Mate1_Direction Quality_Control_Flag Genotype_Short_Name Strain_Isolate_Breed_Ecotype_ID Fragment_Length_Mean Organism Contaminant_Sequences TaxonID Documentation Prepared_By _labkeyurl_Entry_Date Molecule Mate2_Direction Library_preparation_kit Checksum_Raw_FASTQ_Mate1 Cycles Fragment_Length_SD Sample_Name Passage_Number Mate1_5p_Adapter Mate2_3p_Adapter Path_Fastq_Files Mate1_3p_Adapter Treatment_Short_Name Age Sequencing_Date Checksum_Raw_FASTQ_Mate2 Biomaterial_Provider Treatment_Description Sample_Preparation_Date BioAnalyzer_File Sequencing_Instrument Additional_Tissue_Description Protocol_File Name_Quality_Control_File_Mate2 Tissue_Code File_Name_Metadata_File Mate2_File
synthetic_10_reads_paired xxx xxx PAIRED xxx Fri Dec 20 00:00:00 CET 2019 xxx xxx xxx synthetic.mate_1.fastq.gz xxx xxx SENSE xxx xxx xxx 250.0 Homo sapiens xxx 9606 xxx xxx /labkey/Zavolan%20Group/Test_labkey/list-details.view?listId=9&pk=../input_files/project1 xxx ANTISENSE xxx xxx xxx 100.0 synthetic_10_reads_paired xxx AGATCGGAAGAGCGT ../input_files/project1 AGATCGGAAGAGCACA xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx synthetic.mate_2.fastq.gz
synthetic_10_reads_mate_1 xxx xxx SINGLE xxx Fri Dec 20 00:00:00 CET 2019 xxx xxx xxx synthetic.mate_1.fastq.gz xxx xxx SENSE xxx xxx xxx 250.0 Homo sapiens xxx 9606 xxx xxx /labkey/Zavolan%20Group/Test_labkey/list-details.view?listId=9&pk=../input_files/project2 xxx xxx xxx xxx 100.0 synthetic_10_reads_mate_1 xxx ../input_files/project2 AGATCGGAAGAGCACA xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx
--
GitLab