From c4e20a2159325fb7343d5356a8b405cd683f6220 Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Fri, 21 Feb 2020 15:35:08 +0100
Subject: [PATCH] handle polyA processing in input preparation script
- fixes some functions in `labkey_to_snakemake.py`
- add optional argument for trimming polyA tails; they are trimmed as follows:
- if mate is sense, oligo-A is added to sample table for `cutadapt` rule to trim
- if mate is antisense, oligo-T is added to sample table for `cutadapt` rule to trim
- if option is set to `--trim_polya`, oligo-X stretch is added to sample table and `cutadapt` will not trim
---
images/dag_test_workflow.svg | 373 ++++++++++--------
scripts/labkey_to_snakemake.py | 355 +++++++++--------
.../expected_output.md5 | 2 +-
.../expected_output.md5 | 2 +-
4 files changed, 389 insertions(+), 343 deletions(-)
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 6b992f3..9f9e7ad 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,269 +1,318 @@
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-<g id="edge13" class="edge"><title>9->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M690.381,-290.319C701.627,-280.838 715.758,-268.925 728.024,-258.585"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="730.376,-261.18 735.765,-252.058 725.864,-255.828 730.376,-261.18"/>
+<g id="edge13" class="edge">
+<title>9->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M722.78,-290.32C740.95,-280.34 764.02,-267.67 783.49,-256.97"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="785.36,-259.94 792.44,-252.06 781.99,-253.8 785.36,-259.94"/>
</g>
<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1126.5,-252C1126.5,-252 1037.5,-252 1037.5,-252 1031.5,-252 1025.5,-246 1025.5,-240 1025.5,-240 1025.5,-228 1025.5,-228 1025.5,-222 1031.5,-216 1037.5,-216 1037.5,-216 1126.5,-216 1126.5,-216 1132.5,-216 1138.5,-222 1138.5,-228 1138.5,-228 1138.5,-240 1138.5,-240 1138.5,-246 1132.5,-252 1126.5,-252"/>
-<text text-anchor="middle" x="1082" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1237,-252C1237,-252 1136,-252 1136,-252 1130,-252 1124,-246 1124,-240 1124,-240 1124,-228 1124,-228 1124,-222 1130,-216 1136,-216 1136,-216 1237,-216 1237,-216 1243,-216 1249,-222 1249,-228 1249,-228 1249,-240 1249,-240 1249,-246 1243,-252 1237,-252"/>
+<text text-anchor="middle" x="1186.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 9->18 -->
-<g id="edge26" class="edge"><title>9->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M738.35,-290.717C742.959,-289.749 747.541,-288.832 752,-288 865.226,-266.87 898.018,-274.364 1015.13,-252.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1016.06,-255.415 1025.21,-250.075 1014.73,-248.543 1016.06,-255.415"/>
+<g id="edge26" class="edge">
+<title>9->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M767.61,-291.23C773.99,-290.06 780.35,-288.97 786.5,-288 928.12,-265.74 968.19,-276.39 1113.57,-252.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1114.49,-255.42 1123.76,-250.29 1113.32,-248.52 1114.49,-255.42"/>
</g>
<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M541.5,-329C541.5,-329 440.5,-329 440.5,-329 434.5,-329 428.5,-323 428.5,-317 428.5,-317 428.5,-300 428.5,-300 428.5,-294 434.5,-288 440.5,-288 440.5,-288 541.5,-288 541.5,-288 547.5,-288 553.5,-294 553.5,-300 553.5,-300 553.5,-317 553.5,-317 553.5,-323 547.5,-329 541.5,-329"/>
-<text text-anchor="middle" x="491" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="491" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
-<text text-anchor="middle" x="491" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M565,-329C565,-329 450,-329 450,-329 444,-329 438,-323 438,-317 438,-317 438,-300 438,-300 438,-294 444,-288 450,-288 450,-288 565,-288 565,-288 571,-288 577,-294 577,-300 577,-300 577,-317 577,-317 577,-323 571,-329 565,-329"/>
+<text text-anchor="middle" x="507.5" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="507.5" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
+<text text-anchor="middle" x="507.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 10->3 -->
-<g id="edge10" class="edge"><title>10->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M483.076,-287.689C479.859,-279.647 476.094,-270.236 472.644,-261.61"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.891,-260.304 468.928,-252.319 469.392,-262.904 475.891,-260.304"/>
+<g id="edge10" class="edge">
+<title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M504.77,-287.69C503.69,-279.91 502.44,-270.84 501.29,-262.45"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="504.72,-261.75 499.89,-252.32 497.79,-262.7 504.72,-261.75"/>
</g>
<!-- 10->4 -->
-<g id="edge12" class="edge"><title>10->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M520.226,-287.88C533.987,-278.643 550.489,-267.565 564.825,-257.941"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="567.076,-260.646 573.428,-252.166 563.174,-254.834 567.076,-260.646"/>
+<g id="edge12" class="edge">
+<title>10->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M545.93,-287.88C564.79,-278.25 587.57,-266.62 606.95,-256.72"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="608.56,-259.83 615.88,-252.17 605.38,-253.6 608.56,-259.83"/>
</g>
<!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M1015,-326.5C1015,-326.5 919,-326.5 919,-326.5 913,-326.5 907,-320.5 907,-314.5 907,-314.5 907,-302.5 907,-302.5 907,-296.5 913,-290.5 919,-290.5 919,-290.5 1015,-290.5 1015,-290.5 1021,-290.5 1027,-296.5 1027,-302.5 1027,-302.5 1027,-314.5 1027,-314.5 1027,-320.5 1021,-326.5 1015,-326.5"/>
-<text text-anchor="middle" x="967" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1080.5,-326.5C1080.5,-326.5 970.5,-326.5 970.5,-326.5 964.5,-326.5 958.5,-320.5 958.5,-314.5 958.5,-314.5 958.5,-302.5 958.5,-302.5 958.5,-296.5 964.5,-290.5 970.5,-290.5 970.5,-290.5 1080.5,-290.5 1080.5,-290.5 1086.5,-290.5 1092.5,-296.5 1092.5,-302.5 1092.5,-302.5 1092.5,-314.5 1092.5,-314.5 1092.5,-320.5 1086.5,-326.5 1080.5,-326.5"/>
+<text text-anchor="middle" x="1025.5" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 11->4 -->
-<g id="edge11" class="edge"><title>11->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M906.62,-290.63C902.698,-289.695 898.8,-288.808 895,-288 796.444,-267.04 767.467,-272.788 664.451,-251.962"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="665.082,-248.518 654.582,-249.932 663.672,-255.375 665.082,-248.518"/>
+<g id="edge11" class="edge">
+<title>11->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M958.46,-291.13C953.41,-290.03 948.38,-288.97 943.5,-288 848.22,-269.01 820.7,-271.51 722.24,-252.27"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="722.65,-248.78 712.16,-250.27 721.29,-255.65 722.65,-248.78"/>
</g>
<!-- 11->6 -->
-<g id="edge15" class="edge"><title>11->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M958.705,-290.319C954.521,-281.651 949.355,-270.949 944.685,-261.276"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="947.734,-259.542 940.235,-252.058 941.431,-262.585 947.734,-259.542"/>
+<g id="edge15" class="edge">
+<title>11->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1024.32,-290.32C1023.74,-281.92 1023.03,-271.62 1022.37,-262.19"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.86,-261.79 1021.68,-252.06 1018.87,-262.28 1025.86,-261.79"/>
</g>
<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M1241.5,-252C1241.5,-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 1241.5,-216 1241.5,-216 1247.5,-216 1253.5,-222 1253.5,-228 1253.5,-228 1253.5,-240 1253.5,-240 1253.5,-246 1247.5,-252 1241.5,-252"/>
-<text text-anchor="middle" x="1205" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M1362,-252C1362,-252 1279,-252 1279,-252 1273,-252 1267,-246 1267,-240 1267,-240 1267,-228 1267,-228 1267,-222 1273,-216 1279,-216 1279,-216 1362,-216 1362,-216 1368,-216 1374,-222 1374,-228 1374,-228 1374,-240 1374,-240 1374,-246 1368,-252 1362,-252"/>
+<text text-anchor="middle" x="1320.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 11->19 -->
-<g id="edge28" class="edge"><title>11->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1023.1,-290.41C1060.19,-279.112 1108.72,-264.329 1146.32,-252.874"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1147.58,-256.15 1156.13,-249.888 1145.54,-249.454 1147.58,-256.15"/>
+<g id="edge28" class="edge">
+<title>11->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1092.69,-292.13C1136.95,-281.86 1196.4,-267.78 1257.02,-252.34"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.94,-255.72 1266.76,-249.85 1256.21,-248.94 1257.94,-255.72"/>
</g>
<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M873.5,-326.5C873.5,-326.5 772.5,-326.5 772.5,-326.5 766.5,-326.5 760.5,-320.5 760.5,-314.5 760.5,-314.5 760.5,-302.5 760.5,-302.5 760.5,-296.5 766.5,-290.5 772.5,-290.5 772.5,-290.5 873.5,-290.5 873.5,-290.5 879.5,-290.5 885.5,-296.5 885.5,-302.5 885.5,-302.5 885.5,-314.5 885.5,-314.5 885.5,-320.5 879.5,-326.5 873.5,-326.5"/>
-<text text-anchor="middle" x="823" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-<text text-anchor="middle" x="823" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M923,-326.5C923,-326.5 808,-326.5 808,-326.5 802,-326.5 796,-320.5 796,-314.5 796,-314.5 796,-302.5 796,-302.5 796,-296.5 802,-290.5 808,-290.5 808,-290.5 923,-290.5 923,-290.5 929,-290.5 935,-296.5 935,-302.5 935,-302.5 935,-314.5 935,-314.5 935,-320.5 929,-326.5 923,-326.5"/>
+<text text-anchor="middle" x="865.5" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<text text-anchor="middle" x="865.5" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 12->5 -->
-<g id="edge14" class="edge"><title>12->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M807.122,-290.319C798.611,-281.109 787.979,-269.604 778.618,-259.475"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="781.122,-257.027 771.764,-252.058 775.981,-261.778 781.122,-257.027"/>
+<g id="edge14" class="edge">
+<title>12->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M855.55,-290.32C850.47,-281.56 844.2,-270.73 838.55,-260.97"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="841.42,-258.96 833.38,-252.06 835.37,-262.47 841.42,-258.96"/>
</g>
<!-- 12->6 -->
-<g id="edge16" class="edge"><title>12->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M848.831,-290.319C863.492,-280.567 882.022,-268.242 897.868,-257.702"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="899.966,-260.511 906.354,-252.058 896.089,-254.682 899.966,-260.511"/>
+<g id="edge16" class="edge">
+<title>12->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M902.23,-290.32C923.95,-280.16 951.64,-267.21 974.76,-256.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="976.46,-259.47 984.03,-252.06 973.49,-253.12 976.46,-259.47"/>
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<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M962,-180C962,-180 796,-180 796,-180 790,-180 784,-174 784,-168 784,-168 784,-156 784,-156 784,-150 790,-144 796,-144 796,-144 962,-144 962,-144 968,-144 974,-150 974,-156 974,-156 974,-168 974,-168 974,-174 968,-180 962,-180"/>
-<text text-anchor="middle" x="879" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1052,-180C1052,-180 863,-180 863,-180 857,-180 851,-174 851,-168 851,-168 851,-156 851,-156 851,-150 857,-144 863,-144 863,-144 1052,-144 1052,-144 1058,-144 1064,-150 1064,-156 1064,-156 1064,-168 1064,-168 1064,-174 1058,-180 1052,-180"/>
+<text text-anchor="middle" x="957.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 13->7 -->
-<g id="edge17" class="edge"><title>13->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M879,-143.697C879,-135.983 879,-126.712 879,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="882.5,-118.104 879,-108.104 875.5,-118.104 882.5,-118.104"/>
+<g id="edge17" class="edge">
+<title>13->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M957.5,-143.7C957.5,-135.98 957.5,-126.71 957.5,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="961,-118.1 957.5,-108.1 954,-118.1 961,-118.1"/>
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<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M1125.5,-180C1125.5,-180 1004.5,-180 1004.5,-180 998.5,-180 992.5,-174 992.5,-168 992.5,-168 992.5,-156 992.5,-156 992.5,-150 998.5,-144 1004.5,-144 1004.5,-144 1125.5,-144 1125.5,-144 1131.5,-144 1137.5,-150 1137.5,-156 1137.5,-156 1137.5,-168 1137.5,-168 1137.5,-174 1131.5,-180 1125.5,-180"/>
-<text text-anchor="middle" x="1065" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1230.5,-180C1230.5,-180 1094.5,-180 1094.5,-180 1088.5,-180 1082.5,-174 1082.5,-168 1082.5,-168 1082.5,-156 1082.5,-156 1082.5,-150 1088.5,-144 1094.5,-144 1094.5,-144 1230.5,-144 1230.5,-144 1236.5,-144 1242.5,-150 1242.5,-156 1242.5,-156 1242.5,-168 1242.5,-168 1242.5,-174 1236.5,-180 1230.5,-180"/>
+<text text-anchor="middle" x="1162.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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<!-- 14->7 -->
-<g id="edge18" class="edge"><title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1019.5,-143.876C993.62,-134.137 961.033,-121.872 933.759,-111.608"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="934.945,-108.315 924.353,-108.068 932.479,-114.866 934.945,-108.315"/>
+<g id="edge18" class="edge">
+<title>14->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1112.61,-143.97C1083.85,-134.14 1047.49,-121.73 1017.21,-111.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1018.2,-108.03 1007.61,-108.11 1015.94,-114.65 1018.2,-108.03"/>
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<!-- 14->8 -->
-<g id="edge20" class="edge"><title>14->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1065,-143.697C1065,-135.983 1065,-126.712 1065,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1068.5,-118.104 1065,-108.104 1061.5,-118.104 1068.5,-118.104"/>
+<g id="edge20" class="edge">
+<title>14->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1162.5,-143.7C1162.5,-135.98 1162.5,-126.71 1162.5,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1166,-118.1 1162.5,-108.1 1159,-118.1 1166,-118.1"/>
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<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1318,-180C1318,-180 1168,-180 1168,-180 1162,-180 1156,-174 1156,-168 1156,-168 1156,-156 1156,-156 1156,-150 1162,-144 1168,-144 1168,-144 1318,-144 1318,-144 1324,-144 1330,-150 1330,-156 1330,-156 1330,-168 1330,-168 1330,-174 1324,-180 1318,-180"/>
-<text text-anchor="middle" x="1243" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1444.5,-180C1444.5,-180 1272.5,-180 1272.5,-180 1266.5,-180 1260.5,-174 1260.5,-168 1260.5,-168 1260.5,-156 1260.5,-156 1260.5,-150 1266.5,-144 1272.5,-144 1272.5,-144 1444.5,-144 1444.5,-144 1450.5,-144 1456.5,-150 1456.5,-156 1456.5,-156 1456.5,-168 1456.5,-168 1456.5,-174 1450.5,-180 1444.5,-180"/>
+<text text-anchor="middle" x="1358.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
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<!-- 15->8 -->
-<g id="edge19" class="edge"><title>15->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1199.46,-143.876C1174.8,-134.179 1143.78,-121.98 1117.75,-111.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.99,-108.471 1108.4,-108.068 1116.43,-114.985 1118.99,-108.471"/>
+<g id="edge19" class="edge">
+<title>15->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1310.8,-143.97C1283.42,-134.19 1248.84,-121.84 1219.97,-111.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1221,-108.18 1210.41,-108.11 1218.65,-114.77 1221,-108.18"/>
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<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M791,-401C791,-401 523,-401 523,-401 517,-401 511,-395 511,-389 511,-389 511,-377 511,-377 511,-371 517,-365 523,-365 523,-365 791,-365 791,-365 797,-365 803,-371 803,-377 803,-377 803,-389 803,-389 803,-395 797,-401 791,-401"/>
-<text text-anchor="middle" x="657" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="657" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M835,-401C835,-401 534,-401 534,-401 528,-401 522,-395 522,-389 522,-389 522,-377 522,-377 522,-371 528,-365 534,-365 534,-365 835,-365 835,-365 841,-365 847,-371 847,-377 847,-377 847,-389 847,-389 847,-395 841,-401 835,-401"/>
+<text text-anchor="middle" x="684.5" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="684.5" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 16->9 -->
-<g id="edge21" class="edge"><title>16->9</title>
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+<g id="edge21" class="edge">
+<title>16->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M686.16,-364.82C686.97,-356.42 687.96,-346.12 688.88,-336.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="692.38,-336.85 689.85,-326.56 685.41,-336.18 692.38,-336.85"/>
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<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M1113,-401C1113,-401 833,-401 833,-401 827,-401 821,-395 821,-389 821,-389 821,-377 821,-377 821,-371 827,-365 833,-365 833,-365 1113,-365 1113,-365 1119,-365 1125,-371 1125,-377 1125,-377 1125,-389 1125,-389 1125,-395 1119,-401 1113,-401"/>
-<text text-anchor="middle" x="973" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="973" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M1190,-401C1190,-401 877,-401 877,-401 871,-401 865,-395 865,-389 865,-389 865,-377 865,-377 865,-371 871,-365 877,-365 877,-365 1190,-365 1190,-365 1196,-365 1202,-371 1202,-377 1202,-377 1202,-389 1202,-389 1202,-395 1196,-401 1190,-401"/>
+<text text-anchor="middle" x="1033.5" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1033.5" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 17->11 -->
-<g id="edge22" class="edge"><title>17->11</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="972.725,-336.235 968.412,-326.558 965.748,-336.813 972.725,-336.235"/>
+<g id="edge22" class="edge">
+<title>17->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1031.6,-364.82C1030.68,-356.42 1029.54,-346.12 1028.5,-336.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1031.96,-336.11 1027.38,-326.56 1025,-336.88 1031.96,-336.11"/>
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<!-- 18->13 -->
-<g id="edge23" class="edge"><title>18->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1032.6,-215.966C1004.11,-206.142 968.114,-193.729 938.129,-183.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="939.216,-180.062 928.621,-180.111 936.934,-186.68 939.216,-180.062"/>
+<g id="edge23" class="edge">
+<title>18->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1130.77,-215.97C1098.36,-206.06 1057.32,-193.51 1023.32,-183.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1024.06,-179.69 1013.48,-180.11 1022.02,-186.38 1024.06,-179.69"/>
</g>
<!-- 19->15 -->
-<g id="edge24" class="edge"><title>19->15</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1232.02,-190.563 1233.71,-180.104 1225.87,-187.223 1232.02,-190.563"/>
+<g id="edge24" class="edge">
+<title>19->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1329.89,-215.7C1334.26,-207.64 1339.56,-197.89 1344.4,-188.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1347.52,-190.56 1349.21,-180.1 1341.37,-187.22 1347.52,-190.56"/>
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-<path fill="none" stroke="#d6d856" stroke-width="2" d="M1193.5,-329C1193.5,-329 1092.5,-329 1092.5,-329 1086.5,-329 1080.5,-323 1080.5,-317 1080.5,-317 1080.5,-300 1080.5,-300 1080.5,-294 1086.5,-288 1092.5,-288 1092.5,-288 1193.5,-288 1193.5,-288 1199.5,-288 1205.5,-294 1205.5,-300 1205.5,-300 1205.5,-317 1205.5,-317 1205.5,-323 1199.5,-329 1193.5,-329"/>
-<text text-anchor="middle" x="1143" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="1143" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1143" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1311,-329C1311,-329 1196,-329 1196,-329 1190,-329 1184,-323 1184,-317 1184,-317 1184,-300 1184,-300 1184,-294 1190,-288 1196,-288 1196,-288 1311,-288 1311,-288 1317,-288 1323,-294 1323,-300 1323,-300 1323,-317 1323,-317 1323,-323 1317,-329 1311,-329"/>
+<text text-anchor="middle" x="1253.5" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1253.5" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1253.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 20->18 -->
-<g id="edge25" class="edge"><title>20->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1126.33,-287.689C1119.2,-279.215 1110.79,-269.22 1103.22,-260.226"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1105.69,-257.718 1096.57,-252.319 1100.33,-262.225 1105.69,-257.718"/>
+<g id="edge25" class="edge">
+<title>20->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1235.19,-287.69C1227.2,-279.04 1217.75,-268.81 1209.3,-259.68"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1211.86,-257.29 1202.51,-252.32 1206.72,-262.04 1211.86,-257.29"/>
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-<g id="edge27" class="edge"><title>20->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1159.94,-287.689C1167.26,-279.128 1175.91,-269.016 1183.66,-259.951"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1186.35,-262.194 1190.19,-252.319 1181.03,-257.645 1186.35,-262.194"/>
+<g id="edge27" class="edge">
+<title>20->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1271.81,-287.69C1279.8,-279.04 1289.25,-268.81 1297.7,-259.68"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1300.28,-262.04 1304.49,-252.32 1295.14,-257.29 1300.28,-262.04"/>
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</svg>
diff --git a/scripts/labkey_to_snakemake.py b/scripts/labkey_to_snakemake.py
index b6b9569..4456e00 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/scripts/labkey_to_snakemake.py
@@ -1,14 +1,11 @@
#!/usr/bin/env python3
-## -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
# Author : Katsantoni Maria, Christina Herrmann
# Company: Mihaela Zavolan, Biozentrum, Basel
-# -----------------------------------------------------------------------------
-
-# -----------------------------------------------------------------------------
# This script is part of the Zavolan lab quantification pipeline, which is used
-# for analysing RNA-seq data. The table is provided by labkey and is a csv file.
-# If the user provides their own table the table should contain the following
+# for analysing RNA-seq data. The table is provided by labkey as a csv file.
+# If the user provides their own table the table should contain the following
# columns:
# -----------------------------------------------------------------------------
@@ -24,117 +21,95 @@ from Bio import SeqIO
from io import StringIO
from csv import writer
from pathlib import Path
-# for convenience, load QueryFilter explicitly (avoids long lines in filter definitions)
+# (avoids long lines in filter definitions)
from labkey.query import QueryFilter
-# ----------------------------------------------------------------------------------------------------------------------
-def main():
- """ Preprocess sample folder and create config file for snakemake"""
-
- __doc__ = "Preprocess of the table and create config file."
-
- parser = ArgumentParser(
- description=__doc__,
- formatter_class=RawTextHelpFormatter)
- parser.add_argument(
- "genomes_path",
- help="Path containing the FASTA and GTF files for all organisms",
- metavar="GENOMES PATH"
- )
-
- parser.add_argument(
- "--input-table",
- type=str,
- default=None,
- help=(
- "Input table in LabKey format containing the sample information;"
- "\nexactly one of '--input-table' and '--remote' is required."
- ),
- metavar="FILE",
- )
-
- parser.add_argument(
- "--remote",
- action="store_true",
- help=(
- "Fetch LabKey table via API; exactly one of '--input-table' and"
- "\n'--remote' is required."
- ),
- )
-
- parser.add_argument(
- "--project-name",
- help=(
- "Name of LabKey project containing table '--table-name'; required"
- "\nif '--remote' is specified."
- ),
- metavar="STR",
- )
- parser.add_argument(
- "--table-name",
- help="Name of LabKey table; required if '--remote' is specified.",
- metavar="STR",
- )
- parser.add_argument(
- "--input-dict",
- help=(
- "Input dictionary containing the feature name conversion from \n"
- "LabKey to Snakemake; default: '%(default)s'"
- ),
- default=os.path.join(
- os.path.dirname(__file__),
- 'labkey_to_snakemake.dict.tsv'
- ),
- metavar="FILE"
- )
-
- parser.add_argument(
- "--samples-table",
- help="Output table compatible to snakemake; default: '%(default)s'",
- default='samples.tsv',
- metavar="FILE"
- )
-
- parser.add_argument(
- "--multimappers",
- type=int,
- default=100,
- help="Number of allowed multimappers",
- metavar='INT',
- )
-
- parser.add_argument(
- "--soft-clip",
- choices=['EndToEnd','Local'],
- default='EndToEnd',
- help="Soft-clipping option for STAR",
- )
-
- parser.add_argument(
- "--pass-mode",
- choices=['None','Basic'],
- default='None',
- help="2-pass mode option for STAR",
- )
-
- parser.add_argument(
- "--libtype",
- default='A',
- help="Library type for salmon",
- metavar="STR",
- )
-
- parser.add_argument(
- "--config-file",
- help="Configuration file to be used by Snakemake",
- )
+def main():
+ """ Preprocess sample folder and create config file for snakemake"""
+ __doc__ = "Preprocess of labkey table and create " + \
+ "config file and sample table."
+
+ parser = ArgumentParser(description=__doc__,
+ formatter_class=RawTextHelpFormatter)
+
+ parser.add_argument("genomes_path",
+ help="Path containing the FASTA and GTF " +
+ " files for all organisms",
+ metavar="GENOMES PATH")
+
+ parser.add_argument("--input-table",
+ type=str,
+ default=None,
+ help="Input table in LabKey format " +
+ "containing the sample information;" +
+ "\nexactly one '--input-table' and " +
+ "'--remote' is required.",
+ metavar="FILE")
+
+ parser.add_argument("--remote",
+ action="store_true",
+ help="Fetch LabKey table via API; exactly one of " +
+ "'--input-table' and" +
+ "\n'--remote' is required.")
+
+ parser.add_argument("--project-name",
+ help="Name of LabKey project containing table " +
+ " '--table-name'; required" +
+ "\nif '--remote' is specified.",
+ metavar="STR")
+
+ parser.add_argument("--table-name",
+ help="Name of LabKey table; required if '--remote'" +
+ " is specified.",
+ metavar="STR")
+
+ parser.add_argument("--input-dict",
+ help="Input dictionary containing the feature name " +
+ "conversion from LabKey to Snakemake;" +
+ "default: '%(default)s'",
+ default=os.path.join(
+ os.path.dirname(__file__),
+ 'labkey_to_snakemake.dict.tsv'),
+ metavar="FILE")
+
+ parser.add_argument("--samples-table",
+ help="Output table compatible to snakemake;" +
+ "default: '%(default)s'",
+ default='samples.tsv',
+ metavar="FILE")
+
+ parser.add_argument("--trim_polya",
+ type=int,
+ choices=[True, False],
+ default=True,
+ help="Trim poly-As option")
+
+ parser.add_argument("--multimappers",
+ type=int,
+ default=100,
+ help="Number of allowed multimappers",
+ metavar='INT')
+
+ parser.add_argument("--soft-clip",
+ choices=['EndToEnd', 'Local'],
+ default='EndToEnd',
+ help="Soft-clipping option for STAR")
+
+ parser.add_argument("--pass-mode",
+ choices=['None', 'Basic'],
+ default='None',
+ help="2-pass mode option for STAR")
+
+ parser.add_argument("--libtype",
+ default='A',
+ help="Library type for salmon",
+ metavar="STR")
+
+ parser.add_argument("--config-file",
+ help="Configuration file to be used by Snakemake")
- # __________________________________________________________________________________________________________________
- # ------------------------------------------------------------------------------------------------------------------
- # get the arguments
- # ------------------------------------------------------------------------------------------------------------------
try:
options = parser.parse_args()
except(Exception):
@@ -146,27 +121,34 @@ def main():
if options.remote and options.input_table:
parser.print_help()
- print("\n[ERROR] Options '--input-table' and '--remote' are mutually exclusive.")
+ print(
+ "\n[ERROR] Options '--input-table' and ",
+ "'--remote' are mutually exclusive.")
sys.exit(1)
if not options.remote and not options.input_table:
parser.print_help()
- print("\n[ERROR] At least one of '--input-table' and '--remote' is required.")
+ print("\n[ERROR] At least one of '--input-table' ",
+ "and '--remote' is required.")
sys.exit(1)
if options.remote and not options.project_name:
parser.print_help()
- print("\n[ERROR] If option '--remote' is specified, option '--project-name' is required.")
+ print(
+ "\n[ERROR] If option '--remote' is specified, ",
+ "option '--project-name' is required.")
sys.exit(1)
if options.remote and not options.table_name:
parser.print_help()
- print("\n[ERROR] If option '--remote' is specified, option '--table-name' is required.")
+ print(
+ "\n[ERROR] If option '--remote' is specified, ",
+ "option '--table-name' is required.")
sys.exit(1)
sys.stdout.write('Reading input file...\n')
- if options.remote == True:
+ if options.remote is True:
input_table = api_fetch_labkey_table(
project_name=options.project_name,
query_name=options.table_name)
@@ -191,8 +173,11 @@ def main():
input_dict.set_index('snakemake', inplace=True, drop=True)
sys.stdout.write('Create snakemake table...\n')
snakemake_table = pd.DataFrame()
+
for index, row in input_table.iterrows():
- snakemake_table.loc[index, 'sample'] = row[input_dict.loc['replicate_name', 'labkey']] + "_" + row[input_dict.loc['condition', 'labkey']]
+ snakemake_table.loc[index, 'sample'] = row[
+ input_dict.loc['replicate_name', 'labkey']] + "_" + row[
+ input_dict.loc['condition', 'labkey']]
if row[input_dict.loc['seqmode', 'labkey']] == 'PAIRED':
snakemake_table.loc[index, 'seqmode'] = 'paired_end'
elif row[input_dict.loc['seqmode', 'labkey']] == 'SINGLE':
@@ -203,32 +188,16 @@ def main():
row[input_dict.loc['fq1', 'labkey']])
snakemake_table.loc[index, 'fq1'] = fq1
-
- with gzip.open(fq1, "rt") as handle:
- for record in SeqIO.parse(handle, "fastq"):
- read_length = len(record.seq)
- break
-
+ read_length = get_read_length(fq1)
snakemake_table.loc[index, 'index_size'] = read_length
- if read_length <= 50:
- snakemake_table.loc[index, 'kmer'] = 21
- elif read_length > 50:
- snakemake_table.loc[index, 'kmer'] = 31
-
-
- if row[input_dict.loc['seqmode', 'labkey']] == 'PAIRED':
- snakemake_table.loc[index, 'fq2'] = os.path.join(
- row[input_dict.loc['fastq_path', 'labkey']],
- row[input_dict.loc['fq2', 'labkey']])
-
- snakemake_table.loc[index, 'fq1_3p'] = row[input_dict.loc['fq1_3p', 'labkey']]
- snakemake_table.loc[index, 'fq1_5p'] = row[input_dict.loc['fq1_5p', 'labkey']]
-
- if row[input_dict.loc['seqmode', 'labkey']] == 'PAIRED':
- snakemake_table.loc[index, 'fq2_3p'] = row[input_dict.loc['fq2_3p', 'labkey']]
- snakemake_table.loc[index, 'fq2_5p'] = row[input_dict.loc['fq2_5p', 'labkey']]
-
- organism = row[input_dict.loc['organism', 'labkey']].replace(' ', '_').lower()
+ snakemake_table.loc[index, 'kmer'] = infer_kmer_length(read_length)
+ snakemake_table.loc[index, 'fq1_3p'] = row[
+ input_dict.loc['fq1_3p', 'labkey']]
+ snakemake_table.loc[index, 'fq1_5p'] = row[
+ input_dict.loc['fq1_5p', 'labkey']]
+
+ organism = row[input_dict.loc['organism', 'labkey']].replace(
+ ' ', '_').lower()
snakemake_table.loc[index, 'organism'] = organism
snakemake_table.loc[index, 'gtf'] = os.path.join(
@@ -251,39 +220,35 @@ def main():
organism,
'transcriptome.fa')
- snakemake_table.loc[index, 'sd'] = row[input_dict.loc['sd', 'labkey']]
- snakemake_table.loc[index, 'mean'] = row[input_dict.loc['mean', 'labkey']]
+ snakemake_table.loc[index, 'sd'] = row[
+ input_dict.loc['sd', 'labkey']]
+ snakemake_table.loc[index, 'mean'] = row[
+ input_dict.loc['mean', 'labkey']]
snakemake_table.loc[index, 'multimappers'] = options.multimappers
snakemake_table.loc[index, 'soft_clip'] = options.soft_clip
snakemake_table.loc[index, 'pass_mode'] = options.pass_mode
snakemake_table.loc[index, 'libtype'] = options.libtype
-
- if row[input_dict.loc['mate1_direction', 'labkey']] == 'SENSE':
- snakemake_table.loc[index, 'kallisto_directionality'] = '--fr'
- elif row[input_dict.loc['mate1_direction', 'labkey']] == 'ANTISENSE':
- snakemake_table.loc[index, 'kallisto_directionality'] = '--rf'
- else:
- snakemake_table.loc[index, 'kallisto_directionality'] = ''
-
- if row[input_dict.loc['mate1_direction', 'labkey']] == 'SENSE':
- snakemake_table.loc[index, 'fq1_polya'] = 'AAAAAAAAAAAAAAAAA'
- elif row[input_dict.loc['mate1_direction', 'labkey']] == 'ANTISENSE':
- snakemake_table.loc[index, 'fq1_polya'] = 'TTTTTTTTTTTTTTTTT'
- elif row[input_dict.loc['mate1_direction', 'labkey']] == 'RANDOM':
- snakemake_table.loc[index, 'fq1_polya'] = 'AAAAAAAAAAAAAAAAA'
- else:
- pass
+ if options.trim_polya is True:
+ snakemake_table.loc[index, 'fq1_polya'] = trim_polya(
+ row[input_dict.loc['mate1_direction', 'labkey']])
+ snakemake_table.loc[index, 'kallisto_directionality'] = \
+ get_kallisto_directionality(
+ row[input_dict.loc['mate1_direction', 'labkey']])
if row[input_dict.loc['seqmode', 'labkey']] == 'PAIRED':
- if row[input_dict.loc['mate2_direction', 'labkey']] == 'SENSE':
- snakemake_table.loc[index, 'fq2_polya'] = 'AAAAAAAAAAAAAAAAA'
- elif row[input_dict.loc['mate2_direction', 'labkey']] == 'ANTISENSE':
- snakemake_table.loc[index, 'fq2_polya'] = 'TTTTTTTTTTTTTTTTT'
- elif row[input_dict.loc['mate2_direction', 'labkey']] == 'RANDOM':
- snakemake_table.loc[index, 'fq2_polya'] = 'AAAAAAAAAAAAAAAAA'
- else:
- pass
+ fq2 = os.path.join(
+ row[input_dict.loc['fastq_path', 'labkey']],
+ row[input_dict.loc['fq2', 'labkey']])
+ snakemake_table.loc[index, 'fq2'] = fq2
+
+ snakemake_table.loc[index, 'fq2_3p'] = row[
+ input_dict.loc['fq2_3p', 'labkey']]
+ snakemake_table.loc[index, 'fq2_5p'] = row[
+ input_dict.loc['fq2_5p', 'labkey']]
+ if options.trim_polya is True:
+ snakemake_table.loc[index, 'fq2_polya'] = trim_polya(
+ row[input_dict.loc['mate2_direction', 'labkey']])
snakemake_table.fillna('XXXXXXXXXXXXX', inplace=True)
snakemake_table = snakemake_table.astype(
@@ -301,11 +266,10 @@ def main():
header=True,
index=False)
-
# Read file and infer read size for sjdbovwerhang
with open(options.config_file, 'w') as config_file:
config_file.write('''---
- samples: "'''+ options.samples_table + '''"
+ samples: "''' + options.samples_table + '''"
output_dir: "results/"
log_dir: "logs/"
kallisto_indexes: "results/kallisto_indexes/"
@@ -318,19 +282,54 @@ def main():
sys.stdout.write('Create config file finished successfully...\n')
return
+
def api_fetch_labkey_table(project_name=None, query_name=None):
- group_path = os.path.join( '/Zavolan Group', project_name)
- server_context = labkey.utils.create_server_context('labkey.scicore.unibas.ch', group_path, 'labkey', use_ssl=True)
+ group_path = os.path.join('/Zavolan Group', project_name)
+ server_context = labkey.utils.create_server_context(
+ 'labkey.scicore.unibas.ch', group_path, 'labkey', use_ssl=True)
schema_name = "lists"
results = labkey.query.select_rows(server_context, schema_name, query_name)
input_table = pd.DataFrame(results["rows"])
return input_table
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Call the Main function and catch Keyboard interrups
-# -----------------------------------------------------------------------------
+def get_read_length(filename):
+ with gzip.open(filename, "rt") as handle:
+ for record in SeqIO.parse(handle, "fastq"):
+ read_length = len(record.seq)
+ break
+ return read_length
+
+
+def infer_kmer_length(read_length):
+ if read_length <= 50:
+ kmer = 21
+ elif read_length > 50:
+ kmer = 31
+ return kmer
+
+
+def get_kallisto_directionality(directionality):
+ if directionality == 'SENSE':
+ final_direction = '--fr'
+ elif directionality == 'ANTISENSE':
+ final_direction = '--rf'
+ else:
+ final_direction = ''
+ return final_direction
+
+
+def trim_polya(sense):
+ if sense == 'SENSE':
+ polya = 'AAAAAAAAAAAAAAAAA'
+ elif sense == 'ANTISENSE':
+ polya = 'TTTTTTTTTTTTTTTTT'
+ elif sense == 'RANDOM':
+ polya = 'AAAAAAAAAAAAAAAAA'
+ else:
+ polya = 'XXXXXXXXXXXXXXXXX'
+ return polya
+
if __name__ == '__main__':
try:
@@ -338,5 +337,3 @@ if __name__ == '__main__':
except KeyboardInterrupt:
sys.stderr.write("User interrupt!" + os.linesep)
sys.exit(0)
-
-
diff --git a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
index 90bb3be..7708397 100644
--- a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
@@ -1,2 +1,2 @@
ba5ae0649d1fb82d94f8d19481498ffd config.yaml
-9aece9e4acb17143b5e8f627968e03a5 samples.tsv
+cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
\ No newline at end of file
diff --git a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
index 90bb3be..c24f601 100644
--- a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
@@ -1,2 +1,2 @@
ba5ae0649d1fb82d94f8d19481498ffd config.yaml
-9aece9e4acb17143b5e8f627968e03a5 samples.tsv
+cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
--
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