diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 931b3008e9d4253d25531c6bc8e382371807eacb..cf46e51a4789d292723811f51ccc2fdfc4a82f2f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -10,6 +10,7 @@ test:
# add code quality tests here
# add unit tests here
# add script tests here
+ - bash tests/test_scripts_table_to_snakemake/test.sh
- bash tests/test_scripts_labkey_to_snakemake/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
diff --git a/README.md b/README.md
index ba05bcd43633dfeeffa9767fd08be8d9f1f6bf69..d3f693d2780e1030170c0f47fd2b943f5976c489 100644
--- a/README.md
+++ b/README.md
@@ -117,8 +117,8 @@ bash tests/test_integration_workflow/test.slurm.sh
create a directory for your workflow run and traverse inside it with:
```bash
- mkdir runs/my_run
- cd runs/my_run
+ mkdir config/my_run
+ cd config/my_run
```
2. Create empty sample table, workflow configuration and, if necessary, cluster
@@ -224,28 +224,19 @@ you do not have these):
EOF
```
-3. Run the LabKey API client script:
+3. Generate the workflow configuration with the following command, after
+replacing the placeholders with the appropriate values (check out the
+help screen with option '--help' for further options and information):
```bash
- python scripts/labkey_api.py <project_name> <labkey_table_nane>
- ```
-
- > **NOTE:** Right now the script only prints a `pandas` data frame
- > representation of the LabKey table on the screen and manually needs to be
- > saved to a file for the next step. Ultimately the script will produce
- > either a file in table format or will be merged with the following
- > script.
-
-4. Generate the workflow configuration with the following command, after
-replacing the placeholders with the appropriate values:
-
- ```bash
- python scripts scripts/labkey_to_snakemake.py \
- --input_table=<labkey_output_table> \
- --input_dict="scripts/input_dict.tsv" \
- --config_file="runs/my_run/config.yaml" \
- --samples_table="runs/my_run/samples.tsv" \
- --genomes_path=<path_to_annotation_files>
+ python scripts/labkey_to_snakemake.py \
+ --input_dict="scripts/labkey_to_snakemake.dict.tsv" \
+ --config_file="config/my_run/config.yaml" \
+ --samples_table="config/my_run/samples.tsv" \
+ --remote \
+ --project-name="project_name" \
+ --table-name="table_name" \
+ <path_to_annotation_files>
```
#### Additional information
diff --git a/Snakefile b/Snakefile
index c311cd03115dd18c5d12ae8775946c469d323729..2e489ce715d0c905897bee29867c50b89e82f0e6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,5 +1,3 @@
-configfile: "config.yaml"
-
################################################################################
### python modules
################################################################################
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index cd5d63a9a610f30f9303dc59fb2078a33c7d9e21..c53d0db397246b8c51ecff34bdcccf8013f5cd5f 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -4,271 +4,271 @@
<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1408.50 337.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1687pt" height="337pt"
+ viewBox="0.00 0.00 1686.50 337.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 333)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-333 1404.5,-333 1404.5,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-333 1682.5,-333 1682.5,4 -4,4"/>
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-<text text-anchor="middle" x="811.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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-<text text-anchor="middle" x="94.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired</text>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
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+<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
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+<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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-<text text-anchor="middle" x="526.5" y="-87.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M899,-108C899,-108 710,-108 710,-108 704,-108 698,-102 698,-96 698,-96 698,-84 698,-84 698,-78 704,-72 710,-72 710,-72 899,-72 899,-72 905,-72 911,-78 911,-84 911,-84 911,-96 911,-96 911,-102 905,-108 899,-108"/>
+<text text-anchor="middle" x="804.5" y="-87.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="775.43,-31.46 784.31,-25.68 773.76,-24.66 775.43,-31.46"/>
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-<text text-anchor="middle" x="748.5" y="-87.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1112.5,-108C1112.5,-108 940.5,-108 940.5,-108 934.5,-108 928.5,-102 928.5,-96 928.5,-96 928.5,-84 928.5,-84 928.5,-78 934.5,-72 940.5,-72 940.5,-72 1112.5,-72 1112.5,-72 1118.5,-72 1124.5,-78 1124.5,-84 1124.5,-84 1124.5,-96 1124.5,-96 1124.5,-102 1118.5,-108 1112.5,-108"/>
+<text text-anchor="middle" x="1026.5" y="-87.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
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<g id="edge4" class="edge">
<title>4->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="792.02,-45.88 796.11,-36.1 786.81,-41.2 792.02,-45.88"/>
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<g id="node6" class="node">
<title>5</title>
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-<text text-anchor="middle" x="792.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<g id="edge5" class="edge">
<title>5->0</title>
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<title>10</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M691,-180C691,-180 608,-180 608,-180 602,-180 596,-174 596,-168 596,-168 596,-156 596,-156 596,-150 602,-144 608,-144 608,-144 691,-144 691,-144 697,-144 703,-150 703,-156 703,-156 703,-168 703,-168 703,-174 697,-180 691,-180"/>
-<text text-anchor="middle" x="649.5" y="-159.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M969,-180C969,-180 886,-180 886,-180 880,-180 874,-174 874,-168 874,-168 874,-156 874,-156 874,-150 880,-144 886,-144 886,-144 969,-144 969,-144 975,-144 981,-150 981,-156 981,-156 981,-168 981,-168 981,-174 975,-180 969,-180"/>
+<text text-anchor="middle" x="927.5" y="-159.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 10->4 -->
<g id="edge10" class="edge">
<title>10->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M673.72,-143.88C686.42,-134.89 702.16,-123.76 715.92,-114.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="718.04,-116.82 724.19,-108.19 714,-111.11 718.04,-116.82"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M951.72,-143.88C964.42,-134.89 980.16,-123.76 993.92,-114.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="996.04,-116.82 1002.19,-108.19 992,-111.11 996.04,-116.82"/>
</g>
<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M818.5,-254.5C818.5,-254.5 690.5,-254.5 690.5,-254.5 684.5,-254.5 678.5,-248.5 678.5,-242.5 678.5,-242.5 678.5,-230.5 678.5,-230.5 678.5,-224.5 684.5,-218.5 690.5,-218.5 690.5,-218.5 818.5,-218.5 818.5,-218.5 824.5,-218.5 830.5,-224.5 830.5,-230.5 830.5,-230.5 830.5,-242.5 830.5,-242.5 830.5,-248.5 824.5,-254.5 818.5,-254.5"/>
-<text text-anchor="middle" x="754.5" y="-234" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1096.5,-254.5C1096.5,-254.5 968.5,-254.5 968.5,-254.5 962.5,-254.5 956.5,-248.5 956.5,-242.5 956.5,-242.5 956.5,-230.5 956.5,-230.5 956.5,-224.5 962.5,-218.5 968.5,-218.5 968.5,-218.5 1096.5,-218.5 1096.5,-218.5 1102.5,-218.5 1108.5,-224.5 1108.5,-230.5 1108.5,-230.5 1108.5,-242.5 1108.5,-242.5 1108.5,-248.5 1102.5,-254.5 1096.5,-254.5"/>
+<text text-anchor="middle" x="1032.5" y="-234" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 11->5 -->
<g id="edge11" class="edge">
<title>11->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M763.51,-218.32C768.1,-209.56 773.77,-198.73 778.89,-188.97"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="782.02,-190.54 783.56,-180.06 775.82,-187.29 782.02,-190.54"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1041.51,-218.32C1046.1,-209.56 1051.77,-198.73 1056.89,-188.97"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1060.02,-190.54 1061.56,-180.06 1053.82,-187.29 1060.02,-190.54"/>
</g>
<!-- 11->7 -->
<g id="edge15" class="edge">
<title>11->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M828.18,-218.42C832,-217.59 835.8,-216.78 839.5,-216 897.3,-203.88 962.09,-191.5 1014.68,-181.76"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1015.49,-185.17 1024.69,-179.91 1014.22,-178.28 1015.49,-185.17"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1108.81,-220.3C1164.79,-209.15 1241.19,-193.93 1301.19,-181.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1301.93,-185.4 1311.06,-180.02 1300.57,-178.54 1301.93,-185.4"/>
</g>
<!-- 11->9 -->
<g id="edge20" class="edge">
<title>11->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M698.16,-218.41C663.2,-207.8 618.11,-194.13 581.48,-183.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="582.46,-179.65 571.87,-180.1 580.43,-186.35 582.46,-179.65"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M976.16,-218.41C941.2,-207.8 896.11,-194.13 859.48,-183.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="860.46,-179.65 849.87,-180.1 858.43,-186.35 860.46,-179.65"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M976,-257C976,-257 861,-257 861,-257 855,-257 849,-251 849,-245 849,-245 849,-228 849,-228 849,-222 855,-216 861,-216 861,-216 976,-216 976,-216 982,-216 988,-222 988,-228 988,-228 988,-245 988,-245 988,-251 982,-257 976,-257"/>
-<text text-anchor="middle" x="918.5" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="918.5" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
-<text text-anchor="middle" x="918.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1267,-257C1267,-257 1152,-257 1152,-257 1146,-257 1140,-251 1140,-245 1140,-245 1140,-228 1140,-228 1140,-222 1146,-216 1152,-216 1152,-216 1267,-216 1267,-216 1273,-216 1279,-222 1279,-228 1279,-228 1279,-245 1279,-245 1279,-251 1273,-257 1267,-257"/>
+<text text-anchor="middle" x="1209.5" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="1209.5" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
+<text text-anchor="middle" x="1209.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 12->5 -->
<g id="edge12" class="edge">
<title>12->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M884.4,-215.88C868.05,-206.47 848.37,-195.15 831.43,-185.4"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="832.75,-182.12 822.33,-180.17 829.26,-188.19 832.75,-182.12"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1171.88,-215.88C1153.51,-206.29 1131.33,-194.73 1112.41,-184.86"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1113.9,-181.69 1103.41,-180.17 1110.66,-187.89 1113.9,-181.69"/>
</g>
<!-- 12->6 -->
<g id="edge14" class="edge">
<title>12->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M925.6,-215.69C928.46,-207.73 931.79,-198.44 934.86,-189.89"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="938.21,-190.91 938.29,-180.32 931.62,-188.55 938.21,-190.91"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1213.05,-215.69C1214.46,-207.82 1216.11,-198.64 1217.63,-190.17"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.07,-190.78 1219.39,-180.32 1214.18,-189.54 1221.07,-190.78"/>
</g>
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M1128.5,-254.5C1128.5,-254.5 1018.5,-254.5 1018.5,-254.5 1012.5,-254.5 1006.5,-248.5 1006.5,-242.5 1006.5,-242.5 1006.5,-230.5 1006.5,-230.5 1006.5,-224.5 1012.5,-218.5 1018.5,-218.5 1018.5,-218.5 1128.5,-218.5 1128.5,-218.5 1134.5,-218.5 1140.5,-224.5 1140.5,-230.5 1140.5,-230.5 1140.5,-242.5 1140.5,-242.5 1140.5,-248.5 1134.5,-254.5 1128.5,-254.5"/>
-<text text-anchor="middle" x="1073.5" y="-234" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M1427.5,-254.5C1427.5,-254.5 1317.5,-254.5 1317.5,-254.5 1311.5,-254.5 1305.5,-248.5 1305.5,-242.5 1305.5,-242.5 1305.5,-230.5 1305.5,-230.5 1305.5,-224.5 1311.5,-218.5 1317.5,-218.5 1317.5,-218.5 1427.5,-218.5 1427.5,-218.5 1433.5,-218.5 1439.5,-224.5 1439.5,-230.5 1439.5,-230.5 1439.5,-242.5 1439.5,-242.5 1439.5,-248.5 1433.5,-254.5 1427.5,-254.5"/>
+<text text-anchor="middle" x="1372.5" y="-234" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 13->6 -->
<g id="edge13" class="edge">
<title>13->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1042.93,-218.32C1025.18,-208.34 1002.63,-195.67 983.6,-184.97"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="985.28,-181.91 974.85,-180.06 981.85,-188.01 985.28,-181.91"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1336.95,-218.32C1316.03,-208.21 1289.38,-195.33 1267.06,-184.54"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1268.32,-181.26 1257.79,-180.06 1265.27,-187.56 1268.32,-181.26"/>
</g>
<!-- 13->8 -->
<g id="edge17" class="edge">
<title>13->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1130.54,-218.41C1165.95,-207.8 1211.6,-194.13 1248.69,-183.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1249.85,-186.32 1258.42,-180.1 1247.84,-179.62 1249.85,-186.32"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1424.59,-218.41C1456.65,-207.89 1497.91,-194.36 1531.63,-183.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1532.96,-186.54 1541.37,-180.1 1530.78,-179.89 1532.96,-186.54"/>
</g>
<!-- 13->10 -->
<g id="edge22" class="edge">
<title>13->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1009.36,-218.44C1005.36,-217.56 1001.38,-216.74 997.5,-216 875.27,-192.69 839.56,-204.07 713.39,-180.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="713.83,-176.53 703.34,-178.05 712.49,-183.4 713.83,-176.53"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1305.35,-219.41C1299.33,-218.18 1293.32,-217.02 1287.5,-216 1159.72,-193.66 1122.81,-204.81 991.39,-180"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="991.82,-176.52 981.34,-178.07 990.5,-183.4 991.82,-176.52"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M1329,-254.5C1329,-254.5 1214,-254.5 1214,-254.5 1208,-254.5 1202,-248.5 1202,-242.5 1202,-242.5 1202,-230.5 1202,-230.5 1202,-224.5 1208,-218.5 1214,-218.5 1214,-218.5 1329,-218.5 1329,-218.5 1335,-218.5 1341,-224.5 1341,-230.5 1341,-230.5 1341,-242.5 1341,-242.5 1341,-248.5 1335,-254.5 1329,-254.5"/>
-<text text-anchor="middle" x="1271.5" y="-239.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-<text text-anchor="middle" x="1271.5" y="-228.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M1618,-254.5C1618,-254.5 1503,-254.5 1503,-254.5 1497,-254.5 1491,-248.5 1491,-242.5 1491,-242.5 1491,-230.5 1491,-230.5 1491,-224.5 1497,-218.5 1503,-218.5 1503,-218.5 1618,-218.5 1618,-218.5 1624,-218.5 1630,-224.5 1630,-230.5 1630,-230.5 1630,-242.5 1630,-242.5 1630,-248.5 1624,-254.5 1618,-254.5"/>
+<text text-anchor="middle" x="1560.5" y="-239.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<text text-anchor="middle" x="1560.5" y="-228.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 14->7 -->
<g id="edge16" class="edge">
<title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1235.24,-218.32C1213.81,-208.16 1186.48,-195.21 1163.65,-184.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1165.03,-181.18 1154.5,-180.06 1162.04,-187.5 1165.03,-181.18"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1521.63,-218.32C1498.45,-208.07 1468.84,-194.98 1444.24,-184.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1445.65,-180.9 1435.09,-180.06 1442.82,-187.3 1445.65,-180.9"/>
</g>
<!-- 14->8 -->
<g id="edge18" class="edge">
<title>14->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1281.93,-218.32C1287.3,-209.47 1293.95,-198.5 1299.92,-188.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1302.95,-190.42 1305.15,-180.06 1296.97,-186.79 1302.95,-190.42"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1568.32,-218.32C1572.27,-209.65 1577.14,-198.95 1581.54,-189.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1584.78,-190.61 1585.74,-180.06 1578.41,-187.71 1584.78,-190.61"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M623,-257C623,-257 508,-257 508,-257 502,-257 496,-251 496,-245 496,-245 496,-228 496,-228 496,-222 502,-216 508,-216 508,-216 623,-216 623,-216 629,-216 635,-222 635,-228 635,-228 635,-245 635,-245 635,-251 629,-257 623,-257"/>
-<text text-anchor="middle" x="565.5" y="-245" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="565.5" y="-234" font-family="sans" font-size="10.00">index_size: 76</text>
-<text text-anchor="middle" x="565.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M901,-257C901,-257 786,-257 786,-257 780,-257 774,-251 774,-245 774,-245 774,-228 774,-228 774,-222 780,-216 786,-216 786,-216 901,-216 901,-216 907,-216 913,-222 913,-228 913,-228 913,-245 913,-245 913,-251 907,-257 901,-257"/>
+<text text-anchor="middle" x="843.5" y="-245" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="843.5" y="-234" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="843.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 15->9 -->
<g id="edge19" class="edge">
<title>15->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M551.84,-215.69C546.11,-207.39 539.38,-197.63 533.28,-188.78"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="536,-186.56 527.44,-180.32 530.24,-190.54 536,-186.56"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M829.84,-215.69C824.11,-207.39 817.38,-197.63 811.28,-188.78"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="814,-186.56 805.44,-180.32 808.24,-190.54 814,-186.56"/>
</g>
<!-- 15->10 -->
<g id="edge21" class="edge">
<title>15->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M588.45,-215.69C598.85,-206.72 611.22,-196.04 622.1,-186.65"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="624.43,-189.26 629.71,-180.08 619.86,-183.96 624.43,-189.26"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M866.45,-215.69C876.85,-206.72 889.22,-196.04 900.1,-186.65"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="902.43,-189.26 907.71,-180.08 897.86,-183.96 902.43,-189.26"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M837,-329C837,-329 672,-329 672,-329 666,-329 660,-323 660,-317 660,-317 660,-305 660,-305 660,-299 666,-293 672,-293 672,-293 837,-293 837,-293 843,-293 849,-299 849,-305 849,-305 849,-317 849,-317 849,-323 843,-329 837,-329"/>
-<text text-anchor="middle" x="754.5" y="-314" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="754.5" y="-303" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired</text>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M1179,-329C1179,-329 878,-329 878,-329 872,-329 866,-323 866,-317 866,-317 866,-305 866,-305 866,-299 872,-293 878,-293 878,-293 1179,-293 1179,-293 1185,-293 1191,-299 1191,-305 1191,-305 1191,-317 1191,-317 1191,-323 1185,-329 1179,-329"/>
+<text text-anchor="middle" x="1028.5" y="-314" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1028.5" y="-303" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 16->11 -->
<g id="edge23" class="edge">
<title>16->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M754.5,-292.82C754.5,-284.42 754.5,-274.12 754.5,-264.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="758,-264.56 754.5,-254.56 751,-264.56 758,-264.56"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1029.45,-292.82C1029.91,-284.42 1030.48,-274.12 1031,-264.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1034.5,-264.74 1031.56,-254.56 1027.51,-264.35 1034.5,-264.74"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1159,-329C1159,-329 988,-329 988,-329 982,-329 976,-323 976,-317 976,-317 976,-305 976,-305 976,-299 982,-293 988,-293 988,-293 1159,-293 1159,-293 1165,-293 1171,-299 1171,-305 1171,-305 1171,-317 1171,-317 1171,-323 1165,-329 1159,-329"/>
-<text text-anchor="middle" x="1073.5" y="-314" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1073.5" y="-303" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1</text>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1534,-329C1534,-329 1221,-329 1221,-329 1215,-329 1209,-323 1209,-317 1209,-317 1209,-305 1209,-305 1209,-299 1215,-293 1221,-293 1221,-293 1534,-293 1534,-293 1540,-293 1546,-299 1546,-305 1546,-305 1546,-317 1546,-317 1546,-323 1540,-329 1534,-329"/>
+<text text-anchor="middle" x="1377.5" y="-314" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1377.5" y="-303" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 17->13 -->
<g id="edge24" class="edge">
<title>17->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1073.5,-292.82C1073.5,-284.42 1073.5,-274.12 1073.5,-264.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1077,-264.56 1073.5,-254.56 1070,-264.56 1077,-264.56"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1376.32,-292.82C1375.74,-284.42 1375.03,-274.12 1374.37,-264.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1377.86,-264.29 1373.68,-254.56 1370.87,-264.78 1377.86,-264.29"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 54cc82c3cb5a4ebca43644a8cf3e8ad45e7dd0de..11a2f35fcd9d4196628943a4648a1c6e59fdc95b 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -12,17 +12,17 @@
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<title>4</title>
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@@ -90,11 +90,11 @@
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<title>9</title>
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<title>12</title>
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<title>14->8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M946.51,-215.88C964.84,-206.51 987.74,-194.81 1007.33,-184.8"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1009.04,-187.86 1016.36,-180.19 1005.86,-181.62 1009.04,-187.86"/>
@@ -222,17 +222,17 @@
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M353,-252C353,-252 273,-252 273,-252 267,-252 261,-246 261,-240 261,-240 261,-228 261,-228 261,-222 267,-216 273,-216 273,-216 353,-216 353,-216 359,-216 365,-222 365,-228 365,-228 365,-240 365,-240 365,-246 359,-252 353,-252"/>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M353,-252C353,-252 273,-252 273,-252 267,-252 261,-246 261,-240 261,-240 261,-228 261,-228 261,-222 267,-216 273,-216 273,-216 353,-216 353,-216 359,-216 365,-222 365,-228 365,-228 365,-240 365,-240 365,-246 359,-252 353,-252"/>
<text text-anchor="middle" x="313" y="-231.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 15->9 -->
-<g id="edge19" class="edge">
+<g id="edge20" class="edge">
<title>15->9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M297.43,-215.7C289.8,-207.22 280.48,-196.86 272.12,-187.58"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="274.69,-185.2 265.39,-180.1 269.48,-189.88 274.69,-185.2"/>
</g>
<!-- 15->10 -->
-<g id="edge21" class="edge">
+<g id="edge22" class="edge">
<title>15->10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M330.55,-215.7C339.23,-207.14 349.86,-196.66 359.35,-187.3"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="361.99,-189.62 366.65,-180.1 357.07,-184.63 361.99,-189.62"/>
@@ -240,7 +240,7 @@
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M535.5,-324C535.5,-324 392.5,-324 392.5,-324 386.5,-324 380.5,-318 380.5,-312 380.5,-312 380.5,-300 380.5,-300 380.5,-294 386.5,-288 392.5,-288 392.5,-288 535.5,-288 535.5,-288 541.5,-288 547.5,-294 547.5,-300 547.5,-300 547.5,-312 547.5,-312 547.5,-318 541.5,-324 535.5,-324"/>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M535.5,-324C535.5,-324 392.5,-324 392.5,-324 386.5,-324 380.5,-318 380.5,-312 380.5,-312 380.5,-300 380.5,-300 380.5,-294 386.5,-288 392.5,-288 392.5,-288 535.5,-288 535.5,-288 541.5,-288 547.5,-294 547.5,-300 547.5,-300 547.5,-312 547.5,-312 547.5,-318 541.5,-324 535.5,-324"/>
<text text-anchor="middle" x="464" y="-303.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 16->11 -->
@@ -252,7 +252,7 @@
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M828,-324C828,-324 702,-324 702,-324 696,-324 690,-318 690,-312 690,-312 690,-300 690,-300 690,-294 696,-288 702,-288 702,-288 828,-288 828,-288 834,-288 840,-294 840,-300 840,-300 840,-312 840,-312 840,-318 834,-324 828,-324"/>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M828,-324C828,-324 702,-324 702,-324 696,-324 690,-318 690,-312 690,-312 690,-300 690,-300 690,-294 696,-288 702,-288 702,-288 828,-288 828,-288 834,-288 840,-294 840,-300 840,-300 840,-312 840,-312 840,-318 834,-324 828,-324"/>
<text text-anchor="middle" x="765" y="-303.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 17->13 -->
diff --git a/scripts/input_dict_caption.tsv b/scripts/input_dict_caption.tsv
deleted file mode 100644
index 6f043f835084ef9286e1584994f06a40e0011214..0000000000000000000000000000000000000000
--- a/scripts/input_dict_caption.tsv
+++ /dev/null
@@ -1,51 +0,0 @@
-labkey snakemake
-Entry date entry_date
-Path to FASTQ file(s) fastq_path
-Condition name condition
-Replicate name replicate_name
-End type (PAIRED or SINGLE) seqmode
-Name of Mate1 FASTQ file fq1
-Name of Mate2 FASTQ file fq2
-Direction of Mate1 (SENSE, ANTISENSE or RANDOM) mate1_direction
-Direction of Mate2 (SENSE, ANTISENSE or RANDOM) mate2_direction
-5' adapter of Mate1 fq1_5p
-3' adapter of Mate1 fq1_3p
-5' adapter of Mate2 fq2_5p
-3' adapter of Mate2 fq2_3p
-Fragment length mean mean
-Fragment length SD sd
-Quality control flag (PASSED or FAILED) quality_control_flag
-Checksum of raw Mate1 FASTQ file mate1_checksum
-Checksum of raw Mate2 FASTQ file mate2_checksum
-Name of metadata file metadata
-Name of quality control file for Mate1 mate1_quality
-Name of quality control file for Mate2 mate2_quality
-Organism organism
-Taxon ID taxon_id
-Name of Strain / Isolate / Breed / Ecotype strain_name
-Strain / Isolate / Breed / Ecotype ID strain_id
-Biomaterial provider biomaterial_provider
-Source / tissue name source_name
-Tissue code tissue_code
-Additional tissue description tissue_description
-Genotype short name genotype_name
-Genotype description genotype_description
-Disease short name disease_name
-Disease description disease_description
-Abbreviation for treatment treatment
-Treatment description treatment_description
-Gender gender
-Age age
-Developmental stage development_stage
-Passage number passage_number
-Sample preparation date (YYYY-MM-DD) sample_prep_date
-Prepared by prepared_by
-Documentation documentation
-Name of protocol file protocol_file
-Sequencing date (YYYY-MM-DD) seq_date
-Sequencing instrument seq_instrument
-Library preparation kit library_kit
-Cycles cycles
-Molecule molecule
-Contaminant sequences contaminant_seqs
-Name of BioAnalyzer file bioanalyser_file
diff --git a/scripts/input_dict_field_key.tsv b/scripts/labkey_to_snakemake.dict.tsv
similarity index 100%
rename from scripts/input_dict_field_key.tsv
rename to scripts/labkey_to_snakemake.dict.tsv
diff --git a/scripts/labkey_to_snakemake.py b/scripts/labkey_to_snakemake.py
index f0f0ebaffd93a772da63ee7bff982f430545acfa..d39db9c8878acdbbe1b110ba29864076ed8e5d5d 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/scripts/labkey_to_snakemake.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
## -----------------------------------------------------------------------------
# Author : Katsantoni Maria, Christina Herrmann
# Company: Mihaela Zavolan, Biozentrum, Basel
@@ -35,85 +37,98 @@ def main():
formatter_class=RawTextHelpFormatter)
parser.add_argument(
- "--samples_table",
- dest="samples_table",
- help="Output table compatible to snakemake",
- required=True)
-
- parser.add_argument(
- "--input_table",
- dest="input_table",
- help="input table containing the sample information (labkey format)",
- required=True,
- metavar="FILE")
+ "genomes_path",
+ help="Path containing the FASTA and GTF files for all organisms",
+ metavar="GENOMES PATH"
+ )
parser.add_argument(
- "--input_dict",
- dest="input_dict",
- help="input dictionary containing the feature name \
- conversion from labkey to snakemake",
- required=True,
- metavar="FILE")
+ "--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",
- help="Fetch labkey table via API",
- action='store_true')
+ 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 folder containing the labkey table (remote mode)",
- required = False)
+ "--project-name",
+ help=(
+ "Name of LabKey project containing table '--table-name'; required"
+ "\nif '--remote' is specified."
+ ),
+ metavar="STR",
+ )
parser.add_argument(
- "--query_name",
- help="Name of labkey table (remote mode)",
- required = False)
-
+ "--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(
- "--genomes_path",
- dest="genomes_path",
- help="path containing the fasta and gtf files for all organisms",
- required=True)
+ "--samples-table",
+ help="Output table compatible to snakemake; default: '%(default)s'",
+ default='samples.tsv',
+ metavar="FILE"
+ )
parser.add_argument(
"--multimappers",
- dest="multimappers",
- help="number of mulitmappers allowed",
- required=False,
type=int,
- metavar='value',
- default=1)
+ default=100,
+ help="Number of allowed multimappers",
+ metavar='INT',
+ )
parser.add_argument(
- "--soft_clip",
- dest="soft_clip",
- help="soft-clipping option of STAR",
- required=False,
+ "--soft-clip",
choices=['EndToEnd','Local'],
- default='EndToEnd')
+ default='EndToEnd',
+ help="Soft-clipping option for STAR",
+ )
parser.add_argument(
- "--pass_mode",
- dest="pass_mode",
- help="STAR option pass_mode",
- required=False,
+ "--pass-mode",
choices=['None','Basic'],
- default='None')
+ default='None',
+ help="2-pass mode option for STAR",
+ )
parser.add_argument(
"--libtype",
- dest="libtype",
+ default='A',
help="Library type for salmon",
- required=False,
- default='A')
+ metavar="STR",
+ )
parser.add_argument(
- "--config_file",
- dest="config_file",
+ "--config-file",
help="Configuration file to be used by Snakemake",
- required=False)
+ )
# __________________________________________________________________________________________________________________
@@ -129,13 +144,33 @@ def main():
parser.print_help()
sys.exit(1)
+ if options.remote and options.input_table:
+ parser.print_help()
+ 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.")
+ 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.")
+ 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.")
+ sys.exit(1)
+
sys.stdout.write('Reading input file...\n')
if options.remote == True:
input_table = api_fetch_labkey_table(
project_name=options.project_name,
- query_name=options.query_name)
-
+ query_name=options.table_name)
+ input_table.to_csv(options.input_table, sep='\t', index=False)
else:
input_table = pd.read_csv(
options.input_table,
@@ -157,7 +192,7 @@ def main():
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':
@@ -173,7 +208,7 @@ def main():
for record in SeqIO.parse(handle, "fastq"):
read_length = len(record.seq)
break
-
+
snakemake_table.loc[index, 'index_size'] = read_length
if read_length <= 50:
snakemake_table.loc[index, 'kmer'] = 21
@@ -195,7 +230,7 @@ def main():
organism = row[input_dict.loc['organism', 'labkey']].replace(' ', '_').lower()
snakemake_table.loc[index, 'organism'] = organism
-
+
snakemake_table.loc[index, 'gtf'] = os.path.join(
options.genomes_path,
organism,
@@ -251,6 +286,15 @@ def main():
snakemake_table.fillna('XXXXXXXXXXXXX', inplace=True)
+ snakemake_table = snakemake_table.astype(
+ {
+ "sd": int,
+ "mean": int,
+ "multimappers": int,
+ "kmer": int,
+ "index_size": int,
+ }
+ )
snakemake_table.to_csv(
options.samples_table,
sep='\t',
diff --git a/tests/test_integration_workflow/cluster.json b/tests/input_files/cluster.json
similarity index 100%
rename from tests/test_integration_workflow/cluster.json
rename to tests/input_files/cluster.json
diff --git a/tests/input_files/config.yaml b/tests/input_files/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..7697b12bf284d2c9c819610838b64843c8290bc1
--- /dev/null
+++ b/tests/input_files/config.yaml
@@ -0,0 +1,8 @@
+---
+ output_dir: "results"
+ local_log: "local_log"
+ star_indexes: "results/star_indexes"
+ kallisto_indexes: "results/kallisto_indexes"
+ samples: "../input_files/samples.tsv"
+ salmon_indexes: "results/salmon_indexes"
+...
diff --git a/tests/input_files/samples.tsv b/tests/input_files/samples.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..cc0ec82c5caa7d5b7fa0618e80260bc6f2676b92
--- /dev/null
+++ b/tests/input_files/samples.tsv
@@ -0,0 +1,3 @@
+sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya
+synthetic_10_reads_paired_synthetic_10_reads_paired paired_end ../input_files/project1/synthetic.mate_1.fastq.gz 75 31 ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 single_end ../input_files/project2/synthetic.mate_1.fastq.gz 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA XXXXXXXXXXXXX
diff --git a/tests/input_files/synthetic.mate_1.bed b/tests/input_files/synthetic.mate_1.bed
index f838343e902d43817f8d2dabd7c82b7c62a5f755..47335f6a30c2f03477886531c57f6408d2ae391b 100644
--- a/tests/input_files/synthetic.mate_1.bed
+++ b/tests/input_files/synthetic.mate_1.bed
@@ -1,10 +1,10 @@
-1-10000-20000 3397 3472 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + DDX11L1
-1-10000-20000 3249 3324 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + DDX11L1
-1-10000-20000 3735 3810 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + DDX11L1
-1-10000-20000 2055 2130 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + DDX11L1
-1-10000-20000 3567 3642 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + DDX11L1
-1-10000-20000 7920 7995 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - WASH7P
-1-10000-20000 6665 6740 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - WASH7P
-1-10000-20000 6915 6990 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - WASH7P
-1-10000-20000 5841 5916 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - WASH7P
-1-10000-20000 7929 8004 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - WASH7P
+1-10000-20000 3397 3472 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + ENSG00000223972
+1-10000-20000 3249 3324 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + ENSG00000223972
+1-10000-20000 3735 3810 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + ENSG00000223972
+1-10000-20000 2055 2130 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + ENSG00000223972
+1-10000-20000 3567 3642 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + ENSG00000223972
+1-10000-20000 7945 8020 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - ENSG00000227232
+1-10000-20000 6690 6765 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - ENSG00000227232
+1-10000-20000 6940 7015 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - ENSG00000227232
+1-10000-20000 5866 5941 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - ENSG00000227232
+1-10000-20000 7954 8029 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - ENSG00000227232
diff --git a/tests/input_files/synthetic.mate_2.bed b/tests/input_files/synthetic.mate_2.bed
index de4b7133d0fa866c071cdd8d31e522bee5e30bf4..7e09a2d4998b30d045850887089957f08cc1c6f3 100644
--- a/tests/input_files/synthetic.mate_2.bed
+++ b/tests/input_files/synthetic.mate_2.bed
@@ -1,10 +1,10 @@
-1-10000-20000 3422 3497 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + DDX11L1
-1-10000-20000 3274 3349 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + DDX11L1
-1-10000-20000 3760 3835 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + DDX11L1
-1-10000-20000 2080 2155 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + DDX11L1
-1-10000-20000 3592 3667 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + DDX11L1
-1-10000-20000 7945 8020 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - WASH7P
-1-10000-20000 6690 6765 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - WASH7P
-1-10000-20000 6940 7015 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - WASH7P
-1-10000-20000 5866 5941 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - WASH7P
-1-10000-20000 7954 8029 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - WASH7P
+1-10000-20000 3422 3497 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + ENSG00000223972
+1-10000-20000 3274 3349 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + ENSG00000223972
+1-10000-20000 3760 3835 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + ENSG00000223972
+1-10000-20000 2080 2155 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + ENSG00000223972
+1-10000-20000 3592 3667 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + ENSG00000223972
+1-10000-20000 7920 7995 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - ENSG00000227232
+1-10000-20000 6665 6740 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - ENSG00000227232
+1-10000-20000 6915 6990 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - ENSG00000227232
+1-10000-20000 5841 5916 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - ENSG00000227232
+1-10000-20000 7929 8004 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - ENSG00000227232
diff --git a/tests/input_files/synthetic.paired.bed b/tests/input_files/synthetic.paired.bed
deleted file mode 100644
index e372afbf8082916f55425f7cd333fac0da908d55..0000000000000000000000000000000000000000
--- a/tests/input_files/synthetic.paired.bed
+++ /dev/null
@@ -1,10 +0,0 @@
-1-10000-20000 3397 3497 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + DDX11L1
-1-10000-20000 3249 3349 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + DDX11L1
-1-10000-20000 3735 3835 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + DDX11L1
-1-10000-20000 2055 2155 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + DDX11L1
-1-10000-20000 3567 3667 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + DDX11L1
-1-10000-20000 7920 8020 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - WASH7P
-1-10000-20000 6665 6765 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - WASH7P
-1-10000-20000 6915 7015 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - WASH7P
-1-10000-20000 5841 5941 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - WASH7P
-1-10000-20000 7929 8029 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - WASH7P
diff --git a/tests/test_create_dag_image/config.yaml b/tests/test_create_dag_image/config.yaml
deleted file mode 100644
index e1d111b8e0a7f835e0600c476417dd1ce779a9d6..0000000000000000000000000000000000000000
--- a/tests/test_create_dag_image/config.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
----
- ##############################################################################
- ### Annotation
- ##############################################################################
- organism: "Homo_sapiens"
- annotation: "../prepare_annotation/results/annotation.gtf"
- genome: "../prepare_annotation/results/genome.fa"
- annotation_filtered: "../prepare_annotation/results/filtered_transcripts.gtf"
- STAR_index: "../prepare_annotation/results/STAR_index/"
- other_RNAs_sequence: "../prepare_annotation/other.fa"
- other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
- salmon_index: "../prepare_annotation/results/filtered_transcripts_salmon.idx/"
- ##############################################################################
- ### Output and log directories
- ##############################################################################
- database_path: "/some/path"
- STAR_idx_folder: "STAR_indices"
- output_dir: "results"
- star_indexes: "results"
- salmon_indexes: "results"
- kallisto_indexes: "results"
- local_log: "logs/local_log"
- cluster_log: "logs/cluster_log"
-
- ##############################################################################
- ### Sample info
- ##############################################################################
- samples: "samples.tsv"
-...
diff --git a/tests/test_create_dag_image/input_files/chr1-10000-20000.fa b/tests/test_create_dag_image/input_files/chr1-10000-20000.fa
deleted file mode 100644
index 7c6b040a306d1d8c23079ffad83d4cb0f0173959..0000000000000000000000000000000000000000
--- a/tests/test_create_dag_image/input_files/chr1-10000-20000.fa
+++ /dev/null
@@ -1,168 +0,0 @@
->1-10000-20000
-ntaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacc
-ctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccaaccctaaccc
-taaccctaaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctaacc
-taaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccctaacc
-ctaaccctaaaccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaa
-ccccaaccccaaccccaaccccaaccctaacccctaaccctaaccctaaccctaccctaa
-ccctaaccctaaccctaaccctaaccctaacccctaacccctaaccctaaccctaaccct
-aaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctcgcggtaccct
-cagccggcccgcccgcccgggtctgacctgaggagaactgtgctccgccttcagagtacc
-accgaaatctgtgcagaggacaacgcagctccgccctcgcggtgctctccgggtctgtgc
-tgaggagaacgcaactccgccgttgcaaaggcgcgccgcgccggcgcaggcgcagagagg
-cgcgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcg
-cgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcgcg
-ccgcgccggcgcaggcgcagacacatgctagcgcgtcggggtggaggcgtggcgcaggcg
-cagagaggcgcgccgcgccggcgcaggcgcagagacacatgctaccgcgtccaggggtgg
-aggcgtggcgcaggcgcagagaggcgcaccgcgccggcgcaggcgcagagacacatgcta
-gcgcgtccaggggtggaggcgtggcgcaggcgcagagacgcaagcctacgggcgggggtt
-gggggggcgtgtgttgcaggagcaaagtcgcacggcgccgggctggggcggggggagggt
-ggcgccgtgcacgcgcagaaactcacgtcacggtggcgcggcgcagagacgggtagaacc
-tcagtaatccgaaaagccgggatcgaccgccccttgcttgcagccgggcactacaggacc
-cgcttgctcacggtgctgtgccagggcgccccctgctggcgactagggcaactgcagggc
-tctcttgcttagagtggtggccagcgccccctgctggcgccggggcactgcagggccctc
-ttgcttactgtatagtggtggcacgccgcctgctggcagctagggacattgcagggtcct
-cttgctcaaggtgtagtggcagcacgcccacctgctggcagctggggacactgccgggcc
-ctcttgctcCAACAGTACTGGCGGATTATAGGGAAACACCCGGAGCATATGCTGTTTGGT
-CTCAGtagactcctaaatatgggattcctgggtttaaaagtaaaaaataaatatgtttaa
-tttgtgaactgattaccatcagaattgtactgttctgtatcccaccagcaatgtctagga
-atgcctgtttctccacaaagtgtttacttttggatttttgccagtctaacaggtgaAGcc
-ctggagattcttattagtgatttgggctggggcctggccatgtgtatttttttaaatttc
-cactgatgattttgctgcatggccggtgttgagaatgactgCGCAAATTTGCCGGATTTC
-CTTTGCTGTTCCTGCATGTAGTTTAAACGAGATTGCCAGCACCGGGTATCATTCACCATT
-TTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTA
-TTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACA
-GGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGT
-GCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGA
-GTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACA
-ACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAAC
-CTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACGTGGCCGGCCCTCG
-CTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGCCATCGGAGCCCAAAGCCGGGCTGTG
-ACTGCTCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAGGTCTGGCTTTGGCCCTGGGAG
-AGCAGGTGGAAGATCAGGCAGGCCATCGCTGCCACAGAACCCAGTGGATTGGCCTAGGTG
-GGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
-CCGCAGGCACAGCCAAGAGGGCTGAAGAAATGGTAGAACGGAGCAGCTGGTGATGTGTGG
-GCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTT
-CCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGT
-GAGTGTCCCCAGTGTTGCAGAGGTGAGAGGAGAGTAGACAGTGAGTGGGAGTGGCGTCGC
-CCCTAGGGCTCTACGGGGCCGGCGTCTCCTGTCTCCTGGAGAGGCTTCGATGCCCCTCCA
-CACCCTCTTGATCTTCCCTGTGATGTCATCTGGAGCCCTGCTGCTTGCGGTGGCCTATAA
-AGCCTCCTAGTCTGGCTCCAAGGCCTGGCAGAGTCTTTCCCAGGGAAAGCTACAAGCAGC
-AAACAGTCTGCATGGGTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCC
-AAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCC
-TGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAGGGGAGAAGAGGAAAGTGAG
-GTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGA
-GGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCA
-AAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGA
-CACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCAT
-TGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGA
-GATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGA
-CAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGG
-TGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGT
-GGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGG
-GGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCC
-TCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGC
-CTCTGCAGGAGGCTGCCATTTGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCC
-ATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTA
-GTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCC
-CCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGC
-CTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCC
-TCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAA
-GGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTT
-TTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTC
-CTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGAC
-CAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGAT
-CCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTT
-TCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGA
-GCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCT
-TGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAG
-CAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAA
-GGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCT
-GCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCT
-CACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTT
-GGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGG
-ACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCT
-CATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCAC
-TGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCC
-TGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTC
-AGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGAGG
-AGCCACCTCCCAGCCACCTCGGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggg
-gaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagc
-gctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCG
-CATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGT
-CCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTT
-GGCAGTCGAAGAAGATTCTCCTGTCAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCC
-ACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGG
-TGGCGGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCA
-GGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCGATCTTGCCC
-AAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTGCT
-GCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTT
-GGCGGATGGACTCTAGCAGAGTGGCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGC
-TCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGG
-GCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACG
-AGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGTGTGGGGGCCTGGGCACTG
-ACTTCTGCAACCACCTGAGCGCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTA
-GCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCAC
-ACACGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACA
-CAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTTGTTATTAGACCCCTTCTTTC
-CATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCT
-AGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAA
-CAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACC
-CACAGAAAATCCACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTG
-CTCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACA
-GGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggt
-ggtggtgggggcggtgggggtggtgttagtACCCCATCTTGTAGGTCTGAAACACAAAGT
-GTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCC
-AGAACCCAGCTCACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTC
-TGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAG
-GTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG
-GCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGT
-GAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGT
-GGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTG
-CACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCT
-GATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGT
-CTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCG
-ACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCA
-TCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCC
-CCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAG
-GCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGT
-GTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTC
-TTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTT
-CTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGC
-TGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCC
-TCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTATATGCGCGGCCAGCAGACCTGCA
-GGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCA
-GGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAG
-GGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAG
-GCTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGAAGCCTGGGCGAGAAGA
-AAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAA
-ATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTT
-CTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGC
-CTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACA
-GAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGG
-CCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGG
-TGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGACGGTG
-CTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCT
-GAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGA
-TGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAG
-AGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAA
-ATTCAGACGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAGTCC
-CGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggt
-gggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgc
-ttgcatctcatggaacgccatttccccagacatccctgtggctggctccTGATGCCCGAG
-GCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGG
-CCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACAACATCCT
-CCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCC
-ACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCG
-CAGGGAtgagaaggcagaggcgcgactggggttcatgaggaagggcaggaggagggtgtg
-ggatggtggaggggtttgagaaggcagaggcgcgactggggttcatgaggaaagggaggg
-ggaggatgtgggatggtggaggggCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTC
-TAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAAC
-GTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAA
-AGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCT
-GGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTG
-GCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGACCA
-CCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGG
-TCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTG
-GGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCCACAGGGGCAGT
-GGGAGGGAACTGagactggggagggacaaaggctgctctgt
diff --git a/tests/test_create_dag_image/input_files/chr1-10000-20000.gtf b/tests/test_create_dag_image/input_files/chr1-10000-20000.gtf
deleted file mode 100644
index e41d542766ef72a2df834e9e634a62ab061b459c..0000000000000000000000000000000000000000
--- a/tests/test_create_dag_image/input_files/chr1-10000-20000.gtf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!genome-build GRCh38.p13
-#!genome-version GRCh38
-#!genome-date 2013-12
-#!genome-build-accession NCBI:GCA_000001405.28
-#!genebuild-last-updated 2019-08
-1-10000-20000 havana gene 1870 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
-1-10000-20000 havana transcript 1870 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 1870 2228 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 2614 2722 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 3222 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana transcript 2011 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2011 2058 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2180 2228 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2614 2698 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2976 3053 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 3222 3375 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 3454 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana gene 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
-1-10000-20000 havana transcript 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 8269 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7916 8062 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7607 7743 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7234 7369 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 6859 7056 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 6608 6766 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 5797 5948 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 5006 5039 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 4405 4502 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";
diff --git a/tests/test_create_dag_image/input_files/chr1-10000-20000.transcripts.fa b/tests/test_create_dag_image/input_files/chr1-10000-20000.transcripts.fa
deleted file mode 100644
index a55426c270a5458fd5d6c36b723efd8d4cb5b296..0000000000000000000000000000000000000000
--- a/tests/test_create_dag_image/input_files/chr1-10000-20000.transcripts.fa
+++ /dev/null
@@ -1,54 +0,0 @@
->ENST00000456328 gene=DDX11L1
-GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
-GACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA
-GGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG
-TGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAAC
-TTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAA
-CCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACG
-ACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGCAGGGCCATCAGGCACCAAAG
-GGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCC
-TGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTC
-CTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAG
-TTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCT
-CTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGG
-AGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGA
-ATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCA
-ATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTGT
-CCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGT
-TAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCT
-GGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACA
-GCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCT
-CAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCT
-CTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCC
-ATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGG
-GAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCAT
-CCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTG
->ENST00000450305 gene=DDX11L1
-GTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGTTGGAGGAAAGATGAGTGAGAG
-CATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCT
-CCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTCTCAGAGCCCAGGCCAGGGGCCCCCAAG
-AAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAGGGCCATCAGGCACCAA
-AGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGG
-CCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAATTTCAC
-CAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCC
-GCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTG
-TGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCG
-AA
->ENST00000488147 gene=WASH7P
-GTAGAGCAGAGCCGGAGCCAGGTGCAGGCCATTGGAGAGAAGGTCTCCTTGGCCCAGGCCAAGATTGAGA
-AGATCAAGGGCAGCAAGAAGGCCATCAAGGTGTTCTCCAGTGCCAAGTACCCTGCTCCAGGGCGCCTGCA
-GGAATATGGCTCCATCTTCACGGGCGCCCAGGACCCTGGCCTGCAGAGACGCCCCCGCCACAGGATCCAG
-AGCAAGCACCGCCCCCTGGACGAGCGGGCCCTGCAGGAGAAGCTGAAGGACTTTCCTGTGTGCGTGAGCA
-CCAAGCCGGAGCCCGAGGACGATGCAGAAGAGGGACTTGGGGGTCTTCCCAGCAACATCAGCTCTGTCAG
-CTCCTTGCTGCTCTTCAACACCACCGAGAACCTGTAGAAGAAGTATGTCTTCCTGGACCCCCTGGCTGGT
-GCTGTAACAAAGACCCATGTGATGCTGGGGGCAGAGACAGAGGAGAAGCTGTTTGATGCCCCCTTGTCCA
-TCAGCAAGAGAGAGCAGCTGGAACAGCAGGTCCCAGAGAACTACTTCTATGTGCCAGACCTGGGCCAGGT
-GCCTGAGATTGATGTTCCATCCTACCTGCCTGACCTGCCCGGCATTGCCAACGACCTCATGTACATTGCC
-GACCTGGGCCCCGGCATTGCCCCCTCTGCCCCTGGCACCATTCCAGAACTGCCCACCTTCCACACTGAGG
-TAGCCGAGCCTCTCAAGACCTACAAGATGGGGTactaacaccacccccaccgcccccaccaccaccccca
-GCTCCTGAGGTGCTGGCCAGTGCACCCCCACTCCCACCCTCAACCGCGGCCCCTGTAGGCCAAGGCGCCA
-GGCAGGACGACAGCAGCAGCAGCGCGTCTCCTTCAGTCCAGGGAGCTCCCAGGGAAGTGGTTGACCCCTC
-CGGTGGCTGGCCACTCTGCTAGAGTCCATCCGCCAAGCTGGGGGCATCGGCAAGGCCAAGCTGCGCAGCA
-TGAAGGAGCGAAAGCTGGAGAAGCAGCAGCAGAAGGAGCAGGAGCAAGTGAGAGCCACGAGCCAAGGTGG
-GCACTTGATGTCGCTCCATGGGGGGACGGCTCCACCCAGCCTGCGCCACTGTGTTCTTAAGAGGCTTCCA
-GAGAAAACGGCACACCAATCAATAAAGAACTGAGCAGAAA
diff --git a/tests/test_create_dag_image/input_files/synthetic.mate_1.fastq.gz b/tests/test_create_dag_image/input_files/synthetic.mate_1.fastq.gz
deleted file mode 100644
index 6eef226394bbb57b2a0692fde823c4dd252b7fee..0000000000000000000000000000000000000000
Binary files a/tests/test_create_dag_image/input_files/synthetic.mate_1.fastq.gz and /dev/null differ
diff --git a/tests/test_create_dag_image/input_files/synthetic.mate_2.fastq.gz b/tests/test_create_dag_image/input_files/synthetic.mate_2.fastq.gz
deleted file mode 100644
index d48b1cc65d4614ee96a604da5f80f92c99e9bed7..0000000000000000000000000000000000000000
Binary files a/tests/test_create_dag_image/input_files/synthetic.mate_2.fastq.gz and /dev/null differ
diff --git a/tests/test_create_dag_image/samples.tsv b/tests/test_create_dag_image/samples.tsv
deleted file mode 100644
index 3793d813f3f2b9b880904a2aa82c1119a29db84d..0000000000000000000000000000000000000000
--- a/tests/test_create_dag_image/samples.tsv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
-synthetic_10_reads_paired input_files/synthetic.mate_1.fastq.gz input_files/synthetic.mate_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 paired_end
-synthetic_10_reads_mate_1 input_files/synthetic.mate_1.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AAAAAAAAAAAAAAAAAAAA homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 single_end
diff --git a/tests/test_create_dag_image/test.sh b/tests/test_create_dag_image/test.sh
index c377a7e2eb21fb462fee0ef8c35d658b2634cd0c..67bf41ce60e575401a044b2abc402f82ccd97522 100755
--- a/tests/test_create_dag_image/test.sh
+++ b/tests/test_create_dag_image/test.sh
@@ -14,7 +14,7 @@ cd $script_dir
# Run tests
snakemake \
--snakefile="../../Snakefile" \
- --configfile="config.yaml" \
+ --configfile="../input_files/config.yaml" \
--dag \
--printshellcmds \
--dryrun \
diff --git a/tests/test_create_rule_graph/config.yaml b/tests/test_create_rule_graph/config.yaml
deleted file mode 100644
index e1d111b8e0a7f835e0600c476417dd1ce779a9d6..0000000000000000000000000000000000000000
--- a/tests/test_create_rule_graph/config.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
----
- ##############################################################################
- ### Annotation
- ##############################################################################
- organism: "Homo_sapiens"
- annotation: "../prepare_annotation/results/annotation.gtf"
- genome: "../prepare_annotation/results/genome.fa"
- annotation_filtered: "../prepare_annotation/results/filtered_transcripts.gtf"
- STAR_index: "../prepare_annotation/results/STAR_index/"
- other_RNAs_sequence: "../prepare_annotation/other.fa"
- other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
- salmon_index: "../prepare_annotation/results/filtered_transcripts_salmon.idx/"
- ##############################################################################
- ### Output and log directories
- ##############################################################################
- database_path: "/some/path"
- STAR_idx_folder: "STAR_indices"
- output_dir: "results"
- star_indexes: "results"
- salmon_indexes: "results"
- kallisto_indexes: "results"
- local_log: "logs/local_log"
- cluster_log: "logs/cluster_log"
-
- ##############################################################################
- ### Sample info
- ##############################################################################
- samples: "samples.tsv"
-...
diff --git a/tests/test_create_rule_graph/input_files/chr1-10000-20000.fa b/tests/test_create_rule_graph/input_files/chr1-10000-20000.fa
deleted file mode 100644
index 7c6b040a306d1d8c23079ffad83d4cb0f0173959..0000000000000000000000000000000000000000
--- a/tests/test_create_rule_graph/input_files/chr1-10000-20000.fa
+++ /dev/null
@@ -1,168 +0,0 @@
->1-10000-20000
-ntaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacc
-ctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccaaccctaaccc
-taaccctaaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctaacc
-taaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccctaacc
-ctaaccctaaaccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaa
-ccccaaccccaaccccaaccccaaccctaacccctaaccctaaccctaaccctaccctaa
-ccctaaccctaaccctaaccctaaccctaacccctaacccctaaccctaaccctaaccct
-aaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctcgcggtaccct
-cagccggcccgcccgcccgggtctgacctgaggagaactgtgctccgccttcagagtacc
-accgaaatctgtgcagaggacaacgcagctccgccctcgcggtgctctccgggtctgtgc
-tgaggagaacgcaactccgccgttgcaaaggcgcgccgcgccggcgcaggcgcagagagg
-cgcgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcg
-cgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcgcg
-ccgcgccggcgcaggcgcagacacatgctagcgcgtcggggtggaggcgtggcgcaggcg
-cagagaggcgcgccgcgccggcgcaggcgcagagacacatgctaccgcgtccaggggtgg
-aggcgtggcgcaggcgcagagaggcgcaccgcgccggcgcaggcgcagagacacatgcta
-gcgcgtccaggggtggaggcgtggcgcaggcgcagagacgcaagcctacgggcgggggtt
-gggggggcgtgtgttgcaggagcaaagtcgcacggcgccgggctggggcggggggagggt
-ggcgccgtgcacgcgcagaaactcacgtcacggtggcgcggcgcagagacgggtagaacc
-tcagtaatccgaaaagccgggatcgaccgccccttgcttgcagccgggcactacaggacc
-cgcttgctcacggtgctgtgccagggcgccccctgctggcgactagggcaactgcagggc
-tctcttgcttagagtggtggccagcgccccctgctggcgccggggcactgcagggccctc
-ttgcttactgtatagtggtggcacgccgcctgctggcagctagggacattgcagggtcct
-cttgctcaaggtgtagtggcagcacgcccacctgctggcagctggggacactgccgggcc
-ctcttgctcCAACAGTACTGGCGGATTATAGGGAAACACCCGGAGCATATGCTGTTTGGT
-CTCAGtagactcctaaatatgggattcctgggtttaaaagtaaaaaataaatatgtttaa
-tttgtgaactgattaccatcagaattgtactgttctgtatcccaccagcaatgtctagga
-atgcctgtttctccacaaagtgtttacttttggatttttgccagtctaacaggtgaAGcc
-ctggagattcttattagtgatttgggctggggcctggccatgtgtatttttttaaatttc
-cactgatgattttgctgcatggccggtgttgagaatgactgCGCAAATTTGCCGGATTTC
-CTTTGCTGTTCCTGCATGTAGTTTAAACGAGATTGCCAGCACCGGGTATCATTCACCATT
-TTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTA
-TTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACA
-GGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGT
-GCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGA
-GTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACA
-ACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAAC
-CTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACGTGGCCGGCCCTCG
-CTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGCCATCGGAGCCCAAAGCCGGGCTGTG
-ACTGCTCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAGGTCTGGCTTTGGCCCTGGGAG
-AGCAGGTGGAAGATCAGGCAGGCCATCGCTGCCACAGAACCCAGTGGATTGGCCTAGGTG
-GGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
-CCGCAGGCACAGCCAAGAGGGCTGAAGAAATGGTAGAACGGAGCAGCTGGTGATGTGTGG
-GCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTT
-CCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGT
-GAGTGTCCCCAGTGTTGCAGAGGTGAGAGGAGAGTAGACAGTGAGTGGGAGTGGCGTCGC
-CCCTAGGGCTCTACGGGGCCGGCGTCTCCTGTCTCCTGGAGAGGCTTCGATGCCCCTCCA
-CACCCTCTTGATCTTCCCTGTGATGTCATCTGGAGCCCTGCTGCTTGCGGTGGCCTATAA
-AGCCTCCTAGTCTGGCTCCAAGGCCTGGCAGAGTCTTTCCCAGGGAAAGCTACAAGCAGC
-AAACAGTCTGCATGGGTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCC
-AAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCC
-TGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAGGGGAGAAGAGGAAAGTGAG
-GTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGA
-GGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCA
-AAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGA
-CACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCAT
-TGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGA
-GATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGA
-CAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGG
-TGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGT
-GGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGG
-GGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCC
-TCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGC
-CTCTGCAGGAGGCTGCCATTTGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCC
-ATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTA
-GTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCC
-CCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGC
-CTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCC
-TCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAA
-GGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTT
-TTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTC
-CTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGAC
-CAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGAT
-CCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTT
-TCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGA
-GCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCT
-TGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAG
-CAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAA
-GGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCT
-GCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCT
-CACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTT
-GGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGG
-ACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCT
-CATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCAC
-TGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCC
-TGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTC
-AGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGAGG
-AGCCACCTCCCAGCCACCTCGGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggg
-gaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagc
-gctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCG
-CATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGT
-CCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTT
-GGCAGTCGAAGAAGATTCTCCTGTCAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCC
-ACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGG
-TGGCGGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCA
-GGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCGATCTTGCCC
-AAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTGCT
-GCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTT
-GGCGGATGGACTCTAGCAGAGTGGCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGC
-TCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGG
-GCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACG
-AGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGTGTGGGGGCCTGGGCACTG
-ACTTCTGCAACCACCTGAGCGCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTA
-GCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCAC
-ACACGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACA
-CAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTTGTTATTAGACCCCTTCTTTC
-CATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCT
-AGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAA
-CAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACC
-CACAGAAAATCCACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTG
-CTCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACA
-GGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggt
-ggtggtgggggcggtgggggtggtgttagtACCCCATCTTGTAGGTCTGAAACACAAAGT
-GTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCC
-AGAACCCAGCTCACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTC
-TGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAG
-GTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG
-GCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGT
-GAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGT
-GGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTG
-CACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCT
-GATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGT
-CTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCG
-ACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCA
-TCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCC
-CCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAG
-GCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGT
-GTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTC
-TTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTT
-CTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGC
-TGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCC
-TCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTATATGCGCGGCCAGCAGACCTGCA
-GGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCA
-GGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAG
-GGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAG
-GCTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGAAGCCTGGGCGAGAAGA
-AAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAA
-ATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTT
-CTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGC
-CTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACA
-GAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGG
-CCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGG
-TGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGACGGTG
-CTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCT
-GAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGA
-TGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAG
-AGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAA
-ATTCAGACGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAGTCC
-CGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggt
-gggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgc
-ttgcatctcatggaacgccatttccccagacatccctgtggctggctccTGATGCCCGAG
-GCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGG
-CCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACAACATCCT
-CCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCC
-ACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCG
-CAGGGAtgagaaggcagaggcgcgactggggttcatgaggaagggcaggaggagggtgtg
-ggatggtggaggggtttgagaaggcagaggcgcgactggggttcatgaggaaagggaggg
-ggaggatgtgggatggtggaggggCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTC
-TAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAAC
-GTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAA
-AGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCT
-GGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTG
-GCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGACCA
-CCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGG
-TCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTG
-GGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCCACAGGGGCAGT
-GGGAGGGAACTGagactggggagggacaaaggctgctctgt
diff --git a/tests/test_create_rule_graph/input_files/chr1-10000-20000.gtf b/tests/test_create_rule_graph/input_files/chr1-10000-20000.gtf
deleted file mode 100644
index e41d542766ef72a2df834e9e634a62ab061b459c..0000000000000000000000000000000000000000
--- a/tests/test_create_rule_graph/input_files/chr1-10000-20000.gtf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!genome-build GRCh38.p13
-#!genome-version GRCh38
-#!genome-date 2013-12
-#!genome-build-accession NCBI:GCA_000001405.28
-#!genebuild-last-updated 2019-08
-1-10000-20000 havana gene 1870 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
-1-10000-20000 havana transcript 1870 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 1870 2228 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 2614 2722 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 3222 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana transcript 2011 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2011 2058 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2180 2228 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2614 2698 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2976 3053 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 3222 3375 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 3454 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana gene 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
-1-10000-20000 havana transcript 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 8269 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7916 8062 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7607 7743 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7234 7369 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 6859 7056 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 6608 6766 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 5797 5948 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 5006 5039 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 4405 4502 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";
diff --git a/tests/test_create_rule_graph/input_files/chr1-10000-20000.transcripts.fa b/tests/test_create_rule_graph/input_files/chr1-10000-20000.transcripts.fa
deleted file mode 100644
index a55426c270a5458fd5d6c36b723efd8d4cb5b296..0000000000000000000000000000000000000000
--- a/tests/test_create_rule_graph/input_files/chr1-10000-20000.transcripts.fa
+++ /dev/null
@@ -1,54 +0,0 @@
->ENST00000456328 gene=DDX11L1
-GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
-GACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA
-GGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG
-TGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAAC
-TTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAA
-CCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACG
-ACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGCAGGGCCATCAGGCACCAAAG
-GGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCC
-TGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTC
-CTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAG
-TTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCT
-CTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGG
-AGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGA
-ATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCA
-ATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTGT
-CCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGT
-TAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCT
-GGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACA
-GCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCT
-CAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCT
-CTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCC
-ATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGG
-GAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCAT
-CCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTG
->ENST00000450305 gene=DDX11L1
-GTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGTTGGAGGAAAGATGAGTGAGAG
-CATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCT
-CCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTCTCAGAGCCCAGGCCAGGGGCCCCCAAG
-AAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAGGGCCATCAGGCACCAA
-AGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGG
-CCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAATTTCAC
-CAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCC
-GCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTG
-TGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCG
-AA
->ENST00000488147 gene=WASH7P
-GTAGAGCAGAGCCGGAGCCAGGTGCAGGCCATTGGAGAGAAGGTCTCCTTGGCCCAGGCCAAGATTGAGA
-AGATCAAGGGCAGCAAGAAGGCCATCAAGGTGTTCTCCAGTGCCAAGTACCCTGCTCCAGGGCGCCTGCA
-GGAATATGGCTCCATCTTCACGGGCGCCCAGGACCCTGGCCTGCAGAGACGCCCCCGCCACAGGATCCAG
-AGCAAGCACCGCCCCCTGGACGAGCGGGCCCTGCAGGAGAAGCTGAAGGACTTTCCTGTGTGCGTGAGCA
-CCAAGCCGGAGCCCGAGGACGATGCAGAAGAGGGACTTGGGGGTCTTCCCAGCAACATCAGCTCTGTCAG
-CTCCTTGCTGCTCTTCAACACCACCGAGAACCTGTAGAAGAAGTATGTCTTCCTGGACCCCCTGGCTGGT
-GCTGTAACAAAGACCCATGTGATGCTGGGGGCAGAGACAGAGGAGAAGCTGTTTGATGCCCCCTTGTCCA
-TCAGCAAGAGAGAGCAGCTGGAACAGCAGGTCCCAGAGAACTACTTCTATGTGCCAGACCTGGGCCAGGT
-GCCTGAGATTGATGTTCCATCCTACCTGCCTGACCTGCCCGGCATTGCCAACGACCTCATGTACATTGCC
-GACCTGGGCCCCGGCATTGCCCCCTCTGCCCCTGGCACCATTCCAGAACTGCCCACCTTCCACACTGAGG
-TAGCCGAGCCTCTCAAGACCTACAAGATGGGGTactaacaccacccccaccgcccccaccaccaccccca
-GCTCCTGAGGTGCTGGCCAGTGCACCCCCACTCCCACCCTCAACCGCGGCCCCTGTAGGCCAAGGCGCCA
-GGCAGGACGACAGCAGCAGCAGCGCGTCTCCTTCAGTCCAGGGAGCTCCCAGGGAAGTGGTTGACCCCTC
-CGGTGGCTGGCCACTCTGCTAGAGTCCATCCGCCAAGCTGGGGGCATCGGCAAGGCCAAGCTGCGCAGCA
-TGAAGGAGCGAAAGCTGGAGAAGCAGCAGCAGAAGGAGCAGGAGCAAGTGAGAGCCACGAGCCAAGGTGG
-GCACTTGATGTCGCTCCATGGGGGGACGGCTCCACCCAGCCTGCGCCACTGTGTTCTTAAGAGGCTTCCA
-GAGAAAACGGCACACCAATCAATAAAGAACTGAGCAGAAA
diff --git a/tests/test_create_rule_graph/input_files/synthetic.mate_1.fastq.gz b/tests/test_create_rule_graph/input_files/synthetic.mate_1.fastq.gz
deleted file mode 100644
index 6eef226394bbb57b2a0692fde823c4dd252b7fee..0000000000000000000000000000000000000000
Binary files a/tests/test_create_rule_graph/input_files/synthetic.mate_1.fastq.gz and /dev/null differ
diff --git a/tests/test_create_rule_graph/input_files/synthetic.mate_2.fastq.gz b/tests/test_create_rule_graph/input_files/synthetic.mate_2.fastq.gz
deleted file mode 100644
index d48b1cc65d4614ee96a604da5f80f92c99e9bed7..0000000000000000000000000000000000000000
Binary files a/tests/test_create_rule_graph/input_files/synthetic.mate_2.fastq.gz and /dev/null differ
diff --git a/tests/test_create_rule_graph/samples.tsv b/tests/test_create_rule_graph/samples.tsv
deleted file mode 100644
index 3793d813f3f2b9b880904a2aa82c1119a29db84d..0000000000000000000000000000000000000000
--- a/tests/test_create_rule_graph/samples.tsv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
-synthetic_10_reads_paired input_files/synthetic.mate_1.fastq.gz input_files/synthetic.mate_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 paired_end
-synthetic_10_reads_mate_1 input_files/synthetic.mate_1.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AAAAAAAAAAAAAAAAAAAA homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 single_end
diff --git a/tests/test_create_rule_graph/test.sh b/tests/test_create_rule_graph/test.sh
index b67a88800779c5d3d5670d948108562f41bf92e9..00637f5b2b4ede083f3c26e9eb7277fe90a9df92 100755
--- a/tests/test_create_rule_graph/test.sh
+++ b/tests/test_create_rule_graph/test.sh
@@ -14,7 +14,7 @@ cd $script_dir
# Run tests
snakemake \
--snakefile="../../Snakefile" \
- --configfile="config.yaml" \
+ --configfile="../input_files/config.yaml" \
--rulegraph \
--printshellcmds \
--dryrun \
diff --git a/tests/test_integration_workflow/config.yaml b/tests/test_integration_workflow/config.yaml
deleted file mode 100644
index e1d111b8e0a7f835e0600c476417dd1ce779a9d6..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/config.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
----
- ##############################################################################
- ### Annotation
- ##############################################################################
- organism: "Homo_sapiens"
- annotation: "../prepare_annotation/results/annotation.gtf"
- genome: "../prepare_annotation/results/genome.fa"
- annotation_filtered: "../prepare_annotation/results/filtered_transcripts.gtf"
- STAR_index: "../prepare_annotation/results/STAR_index/"
- other_RNAs_sequence: "../prepare_annotation/other.fa"
- other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
- salmon_index: "../prepare_annotation/results/filtered_transcripts_salmon.idx/"
- ##############################################################################
- ### Output and log directories
- ##############################################################################
- database_path: "/some/path"
- STAR_idx_folder: "STAR_indices"
- output_dir: "results"
- star_indexes: "results"
- salmon_indexes: "results"
- kallisto_indexes: "results"
- local_log: "logs/local_log"
- cluster_log: "logs/cluster_log"
-
- ##############################################################################
- ### Sample info
- ##############################################################################
- samples: "samples.tsv"
-...
diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files
index 61c6178473a995ee45db3a364be6ad334b32bf7b..a60f6231a006222654ba30b4109bc60b658c0c99 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -1,132 +1,87 @@
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 4ac2dc973505e6100e3e57055bda88333aa5079a..01c896634a4a0f8e6ddcfeaab13ec9aebfce6562 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -1,132 +1,87 @@
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diff --git a/tests/test_integration_workflow/input_files/chr1-10000-20000.fa b/tests/test_integration_workflow/input_files/chr1-10000-20000.fa
deleted file mode 100644
index 7c6b040a306d1d8c23079ffad83d4cb0f0173959..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/input_files/chr1-10000-20000.fa
+++ /dev/null
@@ -1,168 +0,0 @@
->1-10000-20000
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-TCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAA
-GGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTT
-TTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTC
-CTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGAC
-CAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGAT
-CCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTT
-TCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGA
-GCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCT
-TGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAG
-CAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAA
-GGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCT
-GCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCT
-CACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTT
-GGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGG
-ACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCT
-CATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCAC
-TGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCC
-TGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTC
-AGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGAGG
-AGCCACCTCCCAGCCACCTCGGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggg
-gaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagc
-gctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCG
-CATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGT
-CCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTT
-GGCAGTCGAAGAAGATTCTCCTGTCAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCC
-ACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGG
-TGGCGGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCA
-GGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCGATCTTGCCC
-AAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTGCT
-GCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTT
-GGCGGATGGACTCTAGCAGAGTGGCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGC
-TCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGG
-GCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACG
-AGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGTGTGGGGGCCTGGGCACTG
-ACTTCTGCAACCACCTGAGCGCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTA
-GCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCAC
-ACACGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACA
-CAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTTGTTATTAGACCCCTTCTTTC
-CATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCT
-AGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAA
-CAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACC
-CACAGAAAATCCACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTG
-CTCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACA
-GGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggt
-ggtggtgggggcggtgggggtggtgttagtACCCCATCTTGTAGGTCTGAAACACAAAGT
-GTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCC
-AGAACCCAGCTCACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTC
-TGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAG
-GTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG
-GCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGT
-GAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGT
-GGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTG
-CACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCT
-GATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGT
-CTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCG
-ACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCA
-TCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCC
-CCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAG
-GCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGT
-GTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTC
-TTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTT
-CTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGC
-TGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCC
-TCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTATATGCGCGGCCAGCAGACCTGCA
-GGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCA
-GGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAG
-GGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAG
-GCTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGAAGCCTGGGCGAGAAGA
-AAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAA
-ATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTT
-CTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGC
-CTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACA
-GAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGG
-CCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGG
-TGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGACGGTG
-CTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCT
-GAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGA
-TGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAG
-AGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAA
-ATTCAGACGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAGTCC
-CGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggt
-gggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgc
-ttgcatctcatggaacgccatttccccagacatccctgtggctggctccTGATGCCCGAG
-GCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGG
-CCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACAACATCCT
-CCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCC
-ACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCG
-CAGGGAtgagaaggcagaggcgcgactggggttcatgaggaagggcaggaggagggtgtg
-ggatggtggaggggtttgagaaggcagaggcgcgactggggttcatgaggaaagggaggg
-ggaggatgtgggatggtggaggggCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTC
-TAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAAC
-GTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAA
-AGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCT
-GGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTG
-GCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGACCA
-CCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGG
-TCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTG
-GGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCCACAGGGGCAGT
-GGGAGGGAACTGagactggggagggacaaaggctgctctgt
diff --git a/tests/test_integration_workflow/input_files/chr1-10000-20000.gtf b/tests/test_integration_workflow/input_files/chr1-10000-20000.gtf
deleted file mode 100644
index e41d542766ef72a2df834e9e634a62ab061b459c..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/input_files/chr1-10000-20000.gtf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!genome-build GRCh38.p13
-#!genome-version GRCh38
-#!genome-date 2013-12
-#!genome-build-accession NCBI:GCA_000001405.28
-#!genebuild-last-updated 2019-08
-1-10000-20000 havana gene 1870 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
-1-10000-20000 havana transcript 1870 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 1870 2228 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 2614 2722 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana exon 3222 4410 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000 havana transcript 2011 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2011 2058 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2180 2228 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2614 2698 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 2976 3053 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 3222 3375 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 3454 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana gene 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
-1-10000-20000 havana transcript 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 8269 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7916 8062 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7607 7743 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 7234 7369 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 6859 7056 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 6608 6766 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 5797 5948 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 5006 5039 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana exon 4405 4502 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";
diff --git a/tests/test_integration_workflow/input_files/chr1-10000-20000.transcripts.fa b/tests/test_integration_workflow/input_files/chr1-10000-20000.transcripts.fa
deleted file mode 100644
index a55426c270a5458fd5d6c36b723efd8d4cb5b296..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/input_files/chr1-10000-20000.transcripts.fa
+++ /dev/null
@@ -1,54 +0,0 @@
->ENST00000456328 gene=DDX11L1
-GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
-GACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA
-GGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG
-TGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAAC
-TTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAA
-CCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACG
-ACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGCAGGGCCATCAGGCACCAAAG
-GGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCC
-TGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTC
-CTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAG
-TTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCT
-CTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGG
-AGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGA
-ATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCA
-ATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTGT
-CCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGT
-TAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCT
-GGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACA
-GCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCT
-CAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCT
-CTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCC
-ATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGG
-GAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCAT
-CCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTG
->ENST00000450305 gene=DDX11L1
-GTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGTTGGAGGAAAGATGAGTGAGAG
-CATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCT
-CCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTCTCAGAGCCCAGGCCAGGGGCCCCCAAG
-AAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAGGGCCATCAGGCACCAA
-AGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGG
-CCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAATTTCAC
-CAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCC
-GCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTG
-TGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCG
-AA
->ENST00000488147 gene=WASH7P
-GTAGAGCAGAGCCGGAGCCAGGTGCAGGCCATTGGAGAGAAGGTCTCCTTGGCCCAGGCCAAGATTGAGA
-AGATCAAGGGCAGCAAGAAGGCCATCAAGGTGTTCTCCAGTGCCAAGTACCCTGCTCCAGGGCGCCTGCA
-GGAATATGGCTCCATCTTCACGGGCGCCCAGGACCCTGGCCTGCAGAGACGCCCCCGCCACAGGATCCAG
-AGCAAGCACCGCCCCCTGGACGAGCGGGCCCTGCAGGAGAAGCTGAAGGACTTTCCTGTGTGCGTGAGCA
-CCAAGCCGGAGCCCGAGGACGATGCAGAAGAGGGACTTGGGGGTCTTCCCAGCAACATCAGCTCTGTCAG
-CTCCTTGCTGCTCTTCAACACCACCGAGAACCTGTAGAAGAAGTATGTCTTCCTGGACCCCCTGGCTGGT
-GCTGTAACAAAGACCCATGTGATGCTGGGGGCAGAGACAGAGGAGAAGCTGTTTGATGCCCCCTTGTCCA
-TCAGCAAGAGAGAGCAGCTGGAACAGCAGGTCCCAGAGAACTACTTCTATGTGCCAGACCTGGGCCAGGT
-GCCTGAGATTGATGTTCCATCCTACCTGCCTGACCTGCCCGGCATTGCCAACGACCTCATGTACATTGCC
-GACCTGGGCCCCGGCATTGCCCCCTCTGCCCCTGGCACCATTCCAGAACTGCCCACCTTCCACACTGAGG
-TAGCCGAGCCTCTCAAGACCTACAAGATGGGGTactaacaccacccccaccgcccccaccaccaccccca
-GCTCCTGAGGTGCTGGCCAGTGCACCCCCACTCCCACCCTCAACCGCGGCCCCTGTAGGCCAAGGCGCCA
-GGCAGGACGACAGCAGCAGCAGCGCGTCTCCTTCAGTCCAGGGAGCTCCCAGGGAAGTGGTTGACCCCTC
-CGGTGGCTGGCCACTCTGCTAGAGTCCATCCGCCAAGCTGGGGGCATCGGCAAGGCCAAGCTGCGCAGCA
-TGAAGGAGCGAAAGCTGGAGAAGCAGCAGCAGAAGGAGCAGGAGCAAGTGAGAGCCACGAGCCAAGGTGG
-GCACTTGATGTCGCTCCATGGGGGGACGGCTCCACCCAGCCTGCGCCACTGTGTTCTTAAGAGGCTTCCA
-GAGAAAACGGCACACCAATCAATAAAGAACTGAGCAGAAA
diff --git a/tests/test_integration_workflow/input_files/synthetic.mate_1.bed b/tests/test_integration_workflow/input_files/synthetic.mate_1.bed
deleted file mode 100644
index 47335f6a30c2f03477886531c57f6408d2ae391b..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/input_files/synthetic.mate_1.bed
+++ /dev/null
@@ -1,10 +0,0 @@
-1-10000-20000 3397 3472 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + ENSG00000223972
-1-10000-20000 3249 3324 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + ENSG00000223972
-1-10000-20000 3735 3810 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + ENSG00000223972
-1-10000-20000 2055 2130 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + ENSG00000223972
-1-10000-20000 3567 3642 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + ENSG00000223972
-1-10000-20000 7945 8020 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - ENSG00000227232
-1-10000-20000 6690 6765 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - ENSG00000227232
-1-10000-20000 6940 7015 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - ENSG00000227232
-1-10000-20000 5866 5941 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - ENSG00000227232
-1-10000-20000 7954 8029 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - ENSG00000227232
diff --git a/tests/test_integration_workflow/input_files/synthetic.mate_1.fastq.gz b/tests/test_integration_workflow/input_files/synthetic.mate_1.fastq.gz
deleted file mode 100644
index 6eef226394bbb57b2a0692fde823c4dd252b7fee..0000000000000000000000000000000000000000
Binary files a/tests/test_integration_workflow/input_files/synthetic.mate_1.fastq.gz and /dev/null differ
diff --git a/tests/test_integration_workflow/input_files/synthetic.mate_2.bed b/tests/test_integration_workflow/input_files/synthetic.mate_2.bed
deleted file mode 100644
index 7e09a2d4998b30d045850887089957f08cc1c6f3..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/input_files/synthetic.mate_2.bed
+++ /dev/null
@@ -1,10 +0,0 @@
-1-10000-20000 3422 3497 NS500318:863:HY2KYBGXC:1:11101:14671:1067 0 + ENSG00000223972
-1-10000-20000 3274 3349 NS500318:863:HY2KYBGXC:1:11101:24439:1068 0 + ENSG00000223972
-1-10000-20000 3760 3835 NS500318:863:HY2KYBGXC:1:11101:14965:1069 0 + ENSG00000223972
-1-10000-20000 2080 2155 NS500318:863:HY2KYBGXC:1:11101:21081:1069 0 + ENSG00000223972
-1-10000-20000 3592 3667 NS500318:863:HY2KYBGXC:1:11101:18197:1070 0 + ENSG00000223972
-1-10000-20000 7920 7995 NS500318:863:HY2KYBGXC:1:11101:4614:1071 0 - ENSG00000227232
-1-10000-20000 6665 6740 NS500318:863:HY2KYBGXC:1:11101:8467:1073 0 - ENSG00000227232
-1-10000-20000 6915 6990 NS500318:863:HY2KYBGXC:1:11101:18960:1076 0 - ENSG00000227232
-1-10000-20000 5841 5916 NS500318:863:HY2KYBGXC:1:11101:6851:1076 0 - ENSG00000227232
-1-10000-20000 7929 8004 NS500318:863:HY2KYBGXC:1:11101:14731:1078 0 - ENSG00000227232
diff --git a/tests/test_integration_workflow/input_files/synthetic.mate_2.fastq.gz b/tests/test_integration_workflow/input_files/synthetic.mate_2.fastq.gz
deleted file mode 100644
index d48b1cc65d4614ee96a604da5f80f92c99e9bed7..0000000000000000000000000000000000000000
Binary files a/tests/test_integration_workflow/input_files/synthetic.mate_2.fastq.gz and /dev/null differ
diff --git a/tests/test_integration_workflow/samples.tsv b/tests/test_integration_workflow/samples.tsv
deleted file mode 100644
index 0d242e0516d280185e2fd2b4477edf67a01ad7de..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/samples.tsv
+++ /dev/null
@@ -1,4 +0,0 @@
-sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
-synthetic_10_reads_paired input_files/synthetic.mate_1.fastq.gz input_files/synthetic.mate_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 paired_end
-synthetic_10_reads_mate_1 input_files/synthetic.mate_1.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AAAAAAAAAAAAAAAAAAAA homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 single_end
-synthetic_10_reads_mate_2 input_files/synthetic.mate_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AAAAAAAAAAAAAAAAAAAA homo_sapiens 76 10 Local Basic input_files/chr1-10000-20000.gtf A --fr 250 100 input_files/chr1-10000-20000.fa input_files/chr1-10000-20000.gtf input_files/chr1-10000-20000.transcripts.fa 31 single_end
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index a87ff5856245af3a831078e5c5cb6d9863e85d3f..32923b4fd125c052389ac5dfbb2b7a5571d1b5fd 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# Tear down test environment
-trap 'rm -rf logs/ results/ .snakemake/ && cd $user_dir' EXIT # quoted command is exected after script exits, regardless of exit status
+trap 'rm -rf logs/ results/ .snakemake/ .java/ local_log/ && cd $user_dir' EXIT # quoted command is exected after script exits, regardless of exit status
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
@@ -15,12 +15,12 @@ mkdir -p logs/local_log
# Run tests
snakemake \
--snakefile="../../Snakefile" \
- --configfile="config.yaml" \
+ --configfile="../input_files/config.yaml" \
--cores=4 \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args="--bind ${PWD}"
+ --singularity-args="--bind ${PWD}/../input_files"
# Check md5 sum of some output files
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
@@ -44,24 +44,16 @@ md5sum --check "expected_output.md5"
# as additional option)
echo "Verifying STAR output"
result=$(bedtools intersect -F 1 -v -bed \
- -a input_files/synthetic.mate_1.bed \
- -b results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
+ -a ../input_files/synthetic.mate_1.bed \
+ -b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
exit 1
fi
result=$(bedtools intersect -F 1 -v -bed \
- -a input_files/synthetic.mate_2.bed \
- -b results/single_end/synthetic_10_reads_mate_2/map_genome/synthetic_10_reads_mate_2_Aligned.sortedByCoord.out.bam \
- | wc -l)
-if [ $result != "0" ]; then
- echo "Alignments for mate 1 reads are not consistent with ground truth"
- exit 1
-fi
-result=$(bedtools intersect -F 1 -v -bed \
- -a <(cat input_files/synthetic.mate_1.bed input_files/synthetic.mate_2.bed) \
- -b results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
+ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
+ -b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -71,12 +63,9 @@ fi
# Check whether Salmon assigns reads to expected genes
echo "Verifying Salmon output"
diff \
- <(cat results/single_end/synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
- <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-diff \
- <(cat results/single_end/synthetic_10_reads_mate_2/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
- <(cat input_files/synthetic.mate_2.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+ <(cat results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff \
- <(cat results/paired_end/synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
- <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+ <(cat results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 246a1e506e16cdf03615f7cbff2bc47964a63411..7f773ee11bb7d4d66857d40ca883871983ac3593 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# Tear down test environment
-trap 'rm -rf logs/ results/ .snakemake/ && cd $user_dir' EXIT # quoted command is exected after script exits, regardless of exit status
+trap 'rm -rf logs/ results/ .snakemake/ .java/ local_log/ && cd $user_dir' EXIT # quoted command is exected after script exits, regardless of exit status
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
@@ -16,14 +16,16 @@ mkdir -p logs/local_log
# Run tests
snakemake \
--snakefile="../../Snakefile" \
- --configfile="config.yaml" \
- --cluster-config="cluster.json" \
+ --configfile="../input_files/config.yaml" \
+ --cluster-config="../input_files/cluster.json" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
--cores=256 \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args="--bind ${PWD}"
+ --singularity-args="--bind ${PWD}/../input_files"
+
+# Check md5 sum of some output files
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
md5sum --check "expected_output.md5"
@@ -45,24 +47,16 @@ md5sum --check "expected_output.md5"
# as additional option)
echo "Verifying STAR output"
result=$(bedtools intersect -F 1 -v -bed \
- -a input_files/synthetic.mate_1.bed \
- -b results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
- | wc -l)
-if [ $result != "0" ]; then
- echo "Alignments for mate 1 reads are not consistent with ground truth"
- exit 1
-fi
-result=$(bedtools intersect -F 1 -v -bed \
- -a input_files/synthetic.mate_2.bed \
- -b results/single_end/synthetic_10_reads_mate_2/map_genome/synthetic_10_reads_mate_2_Aligned.sortedByCoord.out.bam \
+ -a ../input_files/synthetic.mate_1.bed \
+ -b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
exit 1
fi
result=$(bedtools intersect -F 1 -v -bed \
- -a <(cat input_files/synthetic.mate_1.bed input_files/synthetic.mate_2.bed) \
- -b results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
+ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
+ -b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -72,12 +66,9 @@ fi
# Check whether Salmon assigns reads to expected genes
echo "Verifying Salmon output"
diff \
- <(cat results/single_end/synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
- <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-diff \
- <(cat results/single_end/synthetic_10_reads_mate_2/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
- <(cat input_files/synthetic.mate_2.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+ <(cat results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff \
- <(cat results/paired_end/synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
- <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+ <(cat results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff --git a/tests/test_scripts_labkey_to_snakemake/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake/expected_output.md5
index 9f6d770457156565d39955f819c437ef641e7343..1dcb38fb810a501c33629ba2105aaed0794bca15 100644
--- a/tests/test_scripts_labkey_to_snakemake/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake/expected_output.md5
@@ -1,2 +1,2 @@
95fb0448dc6871cb415012d254260c5a config.yaml
-4b51a822bcc83ffd744bf76f810162fc samples.tsv
+9aece9e4acb17143b5e8f627968e03a5 samples.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake/input_table.tsv b/tests/test_scripts_labkey_to_snakemake/input_table.tsv
deleted file mode 100644
index f688762bb7620ded05eb5a99abe15b9a96c45048..0000000000000000000000000000000000000000
--- a/tests/test_scripts_labkey_to_snakemake/input_table.tsv
+++ /dev/null
@@ -1,3 +0,0 @@
-Entry date Path to FASTQ file(s) Condition name Replicate name End type (PAIRED or SINGLE) Name of Mate1 FASTQ file Name of Mate2 FASTQ file Direction of Mate1 (SENSE, ANTISENSE or RANDOM) Direction of Mate2 (SENSE, ANTISENSE or RANDOM) 5' adapter of Mate1 3' adapter of Mate1 5' adapter of Mate2 3' adapter of Mate2 Fragment length mean Fragment length SD Quality control flag (PASSED or FAILED) Checksum of raw Mate1 FASTQ file Checksum of raw Mate2 FASTQ file Name of metadata file Name of quality control file for Mate1 Name of quality control file for Mate2 Organism Taxon ID Name of Strain / Isolate / Breed / Ecotype Strain / Isolate / Breed / Ecotype ID Biomaterial provider Source / tissue name Tissue code Additional tissue description Genotype short name Genotype description Disease short name Disease description Abbreviation for treatment Treatment description Gender Age Developmental stage Passage number Sample preparation date (YYYY-MM-DD) Prepared by Documentation Name of protocol file Sequencing date (YYYY-MM-DD) Sequencing instrument Library preparation kit Cycles Molecule Contaminant sequences Name of BioAnalyzer file
-Fri Dec 20 00:00:00 CET 2019 ../input_files/project1 synthetic_10_reads_paired synthetic_10_reads_paired PAIRED synthetic.mate_1.fastq.gz synthetic.mate_2.fastq.gz SENSE ANTISENSE AGATCGGAAGAGCACA AGATCGGAAGAGCGT 250 100 xxx xxx xxx xxx xxx xxx Homo sapiens 9606 xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx
-Fri Dec 20 00:00:00 CET 2019 ../input_files/project2 synthetic_10_reads_mate_1 synthetic_10_reads_mate_1 SINGLE synthetic.mate_1.fastq.gz SENSE AGATCGGAAGAGCACA 250 100 xxx xxx xxx xxx xxx xxx Homo sapiens 9606 xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx
\ No newline at end of file
diff --git a/tests/test_scripts_labkey_to_snakemake/test.sh b/tests/test_scripts_labkey_to_snakemake/test.sh
index a62b53bfa002400989f498a35bc48007a07d3788..c9d1a275909b26286df47ec22914c8669eb26c4c 100755
--- a/tests/test_scripts_labkey_to_snakemake/test.sh
+++ b/tests/test_scripts_labkey_to_snakemake/test.sh
@@ -1,8 +1,11 @@
#!/bin/bash
+# Scripts requires environment variables 'LABKEY_HOST', 'LABKEY_USER' and
+# 'LABKEY_PASS' to be set with the appropriate values
+
# Tear down test environment
-trap 'rm -rf config.yaml samples.tsv .snakemake && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
-#
+trap 'rm -rf ${HOME}/.netrc .snakemake config.yaml samples.tsv input_table.tsv && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
set -u # ensures that script exits when unset variables are used
@@ -11,28 +14,29 @@ user_dir=$PWD
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir
+cat << EOF | ( umask 0377; cat >> ${HOME}/.netrc; )
+machine ${LABKEY_HOST}
+login ${LABKEY_USER}
+password ${LABKEY_PASS}
+EOF
+
# Run tests
python "../../scripts/labkey_to_snakemake.py" \
- --input_table="input_table.tsv" \
- --input_dict="../../scripts/input_dict_caption.tsv" \
- --config_file="config.yaml" \
- --samples_table="samples.tsv" \
- --genomes_path="../input_files" \
+ --input-dict="../../scripts/labkey_to_snakemake.dict.tsv" \
+ --config-file="config.yaml" \
+ --samples-table="samples.tsv" \
--multimappers='10' \
- # --remote \
- # --project_name "TEST_LABKEY" \
- # --query_name "RNA_Seq_data_template"
-
+ --remote \
+ --project-name "TEST_LABKEY" \
+ --table-name "RNA_Seq_data_template" \
+ "../input_files"
+# Check if dry run completes
snakemake \
--snakefile="../../Snakefile" \
--configfile="config.yaml" \
--dryrun \
- # --rulegraph \
- # --printshellcmds \
- # | dot -Tpng > "rulegraph.png"
md5sum --check "expected_output.md5"
-
- # snakemake --rulegraph --configfile config.yaml | dot -Tpng > rulegraph.png
-
+# MD5 sums obtained with command:
+# md5sum config.yaml samples.tsv > expected_output.md5
diff --git a/tests/test_scripts_table_to_snakemake/expected_output.md5 b/tests/test_scripts_table_to_snakemake/expected_output.md5
new file mode 100644
index 0000000000000000000000000000000000000000..1dcb38fb810a501c33629ba2105aaed0794bca15
--- /dev/null
+++ b/tests/test_scripts_table_to_snakemake/expected_output.md5
@@ -0,0 +1,2 @@
+95fb0448dc6871cb415012d254260c5a config.yaml
+9aece9e4acb17143b5e8f627968e03a5 samples.tsv
diff --git a/tests/test_scripts_table_to_snakemake/input_table.tsv b/tests/test_scripts_table_to_snakemake/input_table.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..ee6d5fc45ddff7f69b6ce4a9a97532dd4afb1e72
--- /dev/null
+++ b/tests/test_scripts_table_to_snakemake/input_table.tsv
@@ -0,0 +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
+ 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
diff --git a/tests/test_scripts_table_to_snakemake/test.sh b/tests/test_scripts_table_to_snakemake/test.sh
new file mode 100755
index 0000000000000000000000000000000000000000..63632e054b5c8e4f67aa62cf12e5d44452df9439
--- /dev/null
+++ b/tests/test_scripts_table_to_snakemake/test.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# Tear down test environment
+trap 'rm -rf .snakemake config.yaml samples.tsv && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+python "../../scripts/labkey_to_snakemake.py" \
+ --input-table="input_table.tsv" \
+ --input-dict="../../scripts/labkey_to_snakemake.dict.tsv" \
+ --config-file="config.yaml" \
+ --samples-table="samples.tsv" \
+ --multimappers='10' \
+ "../input_files"
+
+# Check if dry run completes
+snakemake \
+ --snakefile="../../Snakefile" \
+ --configfile="config.yaml" \
+ --dryrun \
+
+md5sum --check "expected_output.md5"
+# MD5 sums obtained with command:
+# md5sum config.yaml samples.tsv > expected_output.md5