From eea0206ff8a9010041853f8ab8b63b2c78981e1b Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Sat, 15 Feb 2020 01:29:44 +0100
Subject: [PATCH] get Snakemake input from LabKey API
- add script that prepares Snakemake input files 'samples.tsv' and 'config.yaml' from LabKey table
- script either connects to API directly (with '--remote' and related options) or processes a tab-separated LabKey dump file
- add tests for both use cases
- common input files for tests now in 'tests/input_files'
- update all other tests to account for new file locations
- update documentation
---
.gitlab-ci.yml | 1 +
README.md | 35 ++-
Snakefile | 2 -
images/dag_test_workflow.svg | 192 +++++++--------
images/rule_graph.svg | 76 +++---
scripts/input_dict_caption.tsv | 51 ----
...d_key.tsv => labkey_to_snakemake.dict.tsv} | 0
scripts/labkey_to_snakemake.py | 156 ++++++++-----
.../cluster.json | 0
tests/input_files/config.yaml | 8 +
tests/input_files/samples.tsv | 3 +
tests/input_files/synthetic.mate_1.bed | 20 +-
tests/input_files/synthetic.mate_2.bed | 20 +-
tests/input_files/synthetic.paired.bed | 10 -
tests/test_create_dag_image/config.yaml | 29 ---
.../input_files/chr1-10000-20000.fa | 168 --------------
.../input_files/chr1-10000-20000.gtf | 28 ---
.../chr1-10000-20000.transcripts.fa | 54 -----
.../input_files/synthetic.mate_1.fastq.gz | Bin 713 -> 0 bytes
.../input_files/synthetic.mate_2.fastq.gz | Bin 710 -> 0 bytes
tests/test_create_dag_image/samples.tsv | 3 -
tests/test_create_dag_image/test.sh | 2 +-
tests/test_create_rule_graph/config.yaml | 29 ---
.../input_files/chr1-10000-20000.fa | 168 --------------
.../input_files/chr1-10000-20000.gtf | 28 ---
.../chr1-10000-20000.transcripts.fa | 54 -----
.../input_files/synthetic.mate_1.fastq.gz | Bin 713 -> 0 bytes
.../input_files/synthetic.mate_2.fastq.gz | Bin 710 -> 0 bytes
tests/test_create_rule_graph/samples.tsv | 3 -
tests/test_create_rule_graph/test.sh | 2 +-
tests/test_integration_workflow/config.yaml | 29 ---
.../expected_output.files | 219 +++++++-----------
.../expected_output.md5 | 219 +++++++-----------
.../input_files/chr1-10000-20000.fa | 168 --------------
.../input_files/chr1-10000-20000.gtf | 28 ---
.../chr1-10000-20000.transcripts.fa | 54 -----
.../input_files/synthetic.mate_1.bed | 10 -
.../input_files/synthetic.mate_1.fastq.gz | Bin 713 -> 0 bytes
.../input_files/synthetic.mate_2.bed | 10 -
.../input_files/synthetic.mate_2.fastq.gz | Bin 710 -> 0 bytes
tests/test_integration_workflow/samples.tsv | 4 -
tests/test_integration_workflow/test.local.sh | 33 +--
tests/test_integration_workflow/test.slurm.sh | 37 ++-
.../expected_output.md5 | 2 +-
.../input_table.tsv | 3 -
.../test_scripts_labkey_to_snakemake/test.sh | 38 +--
.../expected_output.md5 | 2 +
.../input_table.tsv | 3 +
tests/test_scripts_table_to_snakemake/test.sh | 31 +++
49 files changed, 538 insertions(+), 1494 deletions(-)
delete mode 100644 scripts/input_dict_caption.tsv
rename scripts/{input_dict_field_key.tsv => labkey_to_snakemake.dict.tsv} (100%)
rename tests/{test_integration_workflow => input_files}/cluster.json (100%)
create mode 100644 tests/input_files/config.yaml
create mode 100644 tests/input_files/samples.tsv
delete mode 100644 tests/input_files/synthetic.paired.bed
delete mode 100644 tests/test_create_dag_image/config.yaml
delete mode 100644 tests/test_create_dag_image/input_files/chr1-10000-20000.fa
delete mode 100644 tests/test_create_dag_image/input_files/chr1-10000-20000.gtf
delete mode 100644 tests/test_create_dag_image/input_files/chr1-10000-20000.transcripts.fa
delete mode 100644 tests/test_create_dag_image/input_files/synthetic.mate_1.fastq.gz
delete mode 100644 tests/test_create_dag_image/input_files/synthetic.mate_2.fastq.gz
delete mode 100644 tests/test_create_dag_image/samples.tsv
delete mode 100644 tests/test_create_rule_graph/config.yaml
delete mode 100644 tests/test_create_rule_graph/input_files/chr1-10000-20000.fa
delete mode 100644 tests/test_create_rule_graph/input_files/chr1-10000-20000.gtf
delete mode 100644 tests/test_create_rule_graph/input_files/chr1-10000-20000.transcripts.fa
delete mode 100644 tests/test_create_rule_graph/input_files/synthetic.mate_1.fastq.gz
delete mode 100644 tests/test_create_rule_graph/input_files/synthetic.mate_2.fastq.gz
delete mode 100644 tests/test_create_rule_graph/samples.tsv
delete mode 100644 tests/test_integration_workflow/config.yaml
delete mode 100644 tests/test_integration_workflow/input_files/chr1-10000-20000.fa
delete mode 100644 tests/test_integration_workflow/input_files/chr1-10000-20000.gtf
delete mode 100644 tests/test_integration_workflow/input_files/chr1-10000-20000.transcripts.fa
delete mode 100644 tests/test_integration_workflow/input_files/synthetic.mate_1.bed
delete mode 100644 tests/test_integration_workflow/input_files/synthetic.mate_1.fastq.gz
delete mode 100644 tests/test_integration_workflow/input_files/synthetic.mate_2.bed
delete mode 100644 tests/test_integration_workflow/input_files/synthetic.mate_2.fastq.gz
delete mode 100644 tests/test_integration_workflow/samples.tsv
delete mode 100644 tests/test_scripts_labkey_to_snakemake/input_table.tsv
create mode 100644 tests/test_scripts_table_to_snakemake/expected_output.md5
create mode 100644 tests/test_scripts_table_to_snakemake/input_table.tsv
create mode 100755 tests/test_scripts_table_to_snakemake/test.sh
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 931b300..cf46e51 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 ba05bcd..d3f693d 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 c311cd0..2e489ce 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 cd5d63a..c53d0db 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 -->
-<svg width="1409pt" height="337pt"
- 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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+<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="1118.5" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M1478,-180C1478,-180 1315,-180 1315,-180 1309,-180 1303,-174 1303,-168 1303,-168 1303,-156 1303,-156 1303,-150 1309,-144 1315,-144 1315,-144 1478,-144 1478,-144 1484,-144 1490,-150 1490,-156 1490,-156 1490,-168 1490,-168 1490,-174 1484,-180 1478,-180"/>
+<text text-anchor="middle" x="1396.5" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 7->0 -->
<g id="edge7" class="edge">
<title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1081.47,-143.87C1022.25,-116.48 906.93,-63.14 848.03,-35.9"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="849.28,-32.62 838.74,-31.6 846.34,-38.97 849.28,-32.62"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1359.47,-143.87C1300.25,-116.48 1184.93,-63.14 1126.03,-35.9"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1127.28,-32.62 1116.74,-31.6 1124.34,-38.97 1127.28,-32.62"/>
</g>
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M1388.5,-180C1388.5,-180 1242.5,-180 1242.5,-180 1236.5,-180 1230.5,-174 1230.5,-168 1230.5,-168 1230.5,-156 1230.5,-156 1230.5,-150 1236.5,-144 1242.5,-144 1242.5,-144 1388.5,-144 1388.5,-144 1394.5,-144 1400.5,-150 1400.5,-156 1400.5,-156 1400.5,-168 1400.5,-168 1400.5,-174 1394.5,-180 1388.5,-180"/>
-<text text-anchor="middle" x="1315.5" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1666.5,-180C1666.5,-180 1520.5,-180 1520.5,-180 1514.5,-180 1508.5,-174 1508.5,-168 1508.5,-168 1508.5,-156 1508.5,-156 1508.5,-150 1514.5,-144 1520.5,-144 1520.5,-144 1666.5,-144 1666.5,-144 1672.5,-144 1678.5,-150 1678.5,-156 1678.5,-156 1678.5,-168 1678.5,-168 1678.5,-174 1672.5,-180 1666.5,-180"/>
+<text text-anchor="middle" x="1593.5" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 8->0 -->
<g id="edge8" class="edge">
<title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1254.96,-143.94C1149.4,-114.2 934.71,-53.71 848.53,-29.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="849.24,-26 838.67,-26.65 847.34,-32.74 849.24,-26"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1532.96,-143.94C1427.4,-114.2 1212.71,-53.71 1126.53,-29.43"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1127.24,-26 1116.67,-26.65 1125.34,-32.74 1127.24,-26"/>
</g>
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M566,-180C566,-180 465,-180 465,-180 459,-180 453,-174 453,-168 453,-168 453,-156 453,-156 453,-150 459,-144 465,-144 465,-144 566,-144 566,-144 572,-144 578,-150 578,-156 578,-156 578,-168 578,-168 578,-174 572,-180 566,-180"/>
-<text text-anchor="middle" x="515.5" y="-159.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M844,-180C844,-180 743,-180 743,-180 737,-180 731,-174 731,-168 731,-168 731,-156 731,-156 731,-150 737,-144 743,-144 743,-144 844,-144 844,-144 850,-144 856,-150 856,-156 856,-156 856,-168 856,-168 856,-174 850,-180 844,-180"/>
+<text text-anchor="middle" x="793.5" y="-159.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 9->3 -->
<g id="edge9" class="edge">
<title>9->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M518.22,-143.7C519.43,-135.98 520.89,-126.71 522.24,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="525.72,-118.53 523.81,-108.1 518.8,-117.44 525.72,-118.53"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M796.22,-143.7C797.43,-135.98 798.89,-126.71 800.24,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="803.72,-118.53 801.81,-108.1 796.8,-117.44 803.72,-118.53"/>
</g>
<!-- 10 -->
<g id="node11" class="node">
<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"/>
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<!-- 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>
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<!-- 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"/>
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<!-- 14->8 -->
<g id="edge18" class="edge">
<title>14->8</title>
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-<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"/>
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<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
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-<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>
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<!-- 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 54cc82c..11a2f35 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -12,17 +12,17 @@
<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M561,-36C561,-36 531,-36 531,-36 525,-36 519,-30 519,-24 519,-24 519,-12 519,-12 519,-6 525,0 531,0 531,0 561,0 561,0 567,0 573,-6 573,-12 573,-12 573,-24 573,-24 573,-30 567,-36 561,-36"/>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M561,-36C561,-36 531,-36 531,-36 525,-36 519,-30 519,-24 519,-24 519,-12 519,-12 519,-6 525,0 531,0 531,0 561,0 561,0 567,0 573,-6 573,-12 573,-12 573,-24 573,-24 573,-30 567,-36 561,-36"/>
<text text-anchor="middle" x="546" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M52,-108C52,-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 52,-72 52,-72 58,-72 64,-78 64,-84 64,-84 64,-96 64,-96 64,-102 58,-108 52,-108"/>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M52,-108C52,-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 52,-72 52,-72 58,-72 64,-78 64,-84 64,-84 64,-96 64,-96 64,-102 58,-108 52,-108"/>
<text text-anchor="middle" x="32" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge6" class="edge">
+<g id="edge3" class="edge">
<title>1->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M64.39,-74.6C67.27,-73.62 70.16,-72.73 73,-72 231.51,-31.13 427.95,-21.78 508.69,-19.64"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="508.94,-23.13 518.85,-19.39 508.77,-16.13 508.94,-23.13"/>
@@ -30,11 +30,11 @@
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M124,-108C124,-108 94,-108 94,-108 88,-108 82,-102 82,-96 82,-96 82,-84 82,-84 82,-78 88,-72 94,-72 94,-72 124,-72 124,-72 130,-72 136,-78 136,-84 136,-84 136,-96 136,-96 136,-102 130,-108 124,-108"/>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M124,-108C124,-108 94,-108 94,-108 88,-108 82,-102 82,-96 82,-96 82,-84 82,-84 82,-78 88,-72 94,-72 94,-72 124,-72 124,-72 130,-72 136,-78 136,-84 136,-84 136,-96 136,-96 136,-102 130,-108 124,-108"/>
<text text-anchor="middle" x="109" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 2->0 -->
-<g id="edge5" class="edge">
+<g id="edge8" class="edge">
<title>2->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M136.17,-75.1C139.1,-73.92 142.08,-72.86 145,-72 274.75,-33.8 436.26,-23.08 508.28,-20.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="508.79,-23.6 518.65,-19.72 508.53,-16.6 508.79,-23.6"/>
@@ -42,11 +42,11 @@
<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M355.5,-108C355.5,-108 166.5,-108 166.5,-108 160.5,-108 154.5,-102 154.5,-96 154.5,-96 154.5,-84 154.5,-84 154.5,-78 160.5,-72 166.5,-72 166.5,-72 355.5,-72 355.5,-72 361.5,-72 367.5,-78 367.5,-84 367.5,-84 367.5,-96 367.5,-96 367.5,-102 361.5,-108 355.5,-108"/>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M355.5,-108C355.5,-108 166.5,-108 166.5,-108 160.5,-108 154.5,-102 154.5,-96 154.5,-96 154.5,-84 154.5,-84 154.5,-78 160.5,-72 166.5,-72 166.5,-72 355.5,-72 355.5,-72 361.5,-72 367.5,-78 367.5,-84 367.5,-84 367.5,-96 367.5,-96 367.5,-102 361.5,-108 355.5,-108"/>
<text text-anchor="middle" x="261" y="-87.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 3->0 -->
-<g id="edge2" class="edge">
+<g id="edge4" class="edge">
<title>3->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M330.35,-71.97C386.61,-58.15 463.72,-39.21 508.87,-28.12"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="509.93,-31.46 518.81,-25.68 508.26,-24.66 509.93,-31.46"/>
@@ -54,11 +54,11 @@
<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M569,-108C569,-108 397,-108 397,-108 391,-108 385,-102 385,-96 385,-96 385,-84 385,-84 385,-78 391,-72 397,-72 397,-72 569,-72 569,-72 575,-72 581,-78 581,-84 581,-84 581,-96 581,-96 581,-102 575,-108 569,-108"/>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M569,-108C569,-108 397,-108 397,-108 391,-108 385,-102 385,-96 385,-96 385,-84 385,-84 385,-78 391,-72 397,-72 397,-72 569,-72 569,-72 575,-72 581,-78 581,-84 581,-84 581,-96 581,-96 581,-102 575,-108 569,-108"/>
<text text-anchor="middle" x="483" y="-87.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 4->0 -->
-<g id="edge1" class="edge">
+<g id="edge6" class="edge">
<title>4->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M498.57,-71.7C506.2,-63.22 515.52,-52.86 523.88,-43.58"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="526.52,-45.88 530.61,-36.1 521.31,-41.2 526.52,-45.88"/>
@@ -66,11 +66,11 @@
<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M586,-180C586,-180 468,-180 468,-180 462,-180 456,-174 456,-168 456,-168 456,-156 456,-156 456,-150 462,-144 468,-144 468,-144 586,-144 586,-144 592,-144 598,-150 598,-156 598,-156 598,-168 598,-168 598,-174 592,-180 586,-180"/>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M586,-180C586,-180 468,-180 468,-180 462,-180 456,-174 456,-168 456,-168 456,-156 456,-156 456,-150 462,-144 468,-144 468,-144 586,-144 586,-144 592,-144 598,-150 598,-156 598,-156 598,-168 598,-168 598,-174 592,-180 586,-180"/>
<text text-anchor="middle" x="527" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 5->0 -->
-<g id="edge7" class="edge">
+<g id="edge5" class="edge">
<title>5->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M557.3,-143.8C569.88,-134.9 583.12,-122.77 590,-108 596.75,-93.49 595.43,-87.05 590,-72 586.25,-61.6 579.46,-51.8 572.33,-43.52"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="574.83,-41.06 565.47,-36.08 569.68,-45.81 574.83,-41.06"/>
@@ -78,11 +78,11 @@
<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M729.5,-180C729.5,-180 628.5,-180 628.5,-180 622.5,-180 616.5,-174 616.5,-168 616.5,-168 616.5,-156 616.5,-156 616.5,-150 622.5,-144 628.5,-144 628.5,-144 729.5,-144 729.5,-144 735.5,-144 741.5,-150 741.5,-156 741.5,-156 741.5,-168 741.5,-168 741.5,-174 735.5,-180 729.5,-180"/>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M729.5,-180C729.5,-180 628.5,-180 628.5,-180 622.5,-180 616.5,-174 616.5,-168 616.5,-168 616.5,-156 616.5,-156 616.5,-150 622.5,-144 628.5,-144 628.5,-144 729.5,-144 729.5,-144 735.5,-144 741.5,-150 741.5,-156 741.5,-156 741.5,-168 741.5,-168 741.5,-174 735.5,-180 729.5,-180"/>
<text text-anchor="middle" x="679" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 6->0 -->
-<g id="edge4" class="edge">
+<g id="edge2" class="edge">
<title>6->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M666.56,-143.86C652.82,-125.38 629.64,-95.45 607,-72 597.14,-61.79 585.54,-51.36 575.12,-42.5"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="577.34,-39.79 567.43,-36.05 572.84,-45.15 577.34,-39.79"/>
@@ -90,11 +90,11 @@
<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M934.5,-180C934.5,-180 771.5,-180 771.5,-180 765.5,-180 759.5,-174 759.5,-168 759.5,-168 759.5,-156 759.5,-156 759.5,-150 765.5,-144 771.5,-144 771.5,-144 934.5,-144 934.5,-144 940.5,-144 946.5,-150 946.5,-156 946.5,-156 946.5,-168 946.5,-168 946.5,-174 940.5,-180 934.5,-180"/>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M934.5,-180C934.5,-180 771.5,-180 771.5,-180 765.5,-180 759.5,-174 759.5,-168 759.5,-168 759.5,-156 759.5,-156 759.5,-150 765.5,-144 771.5,-144 771.5,-144 934.5,-144 934.5,-144 940.5,-144 946.5,-150 946.5,-156 946.5,-156 946.5,-168 946.5,-168 946.5,-174 940.5,-180 934.5,-180"/>
<text text-anchor="middle" x="853" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 7->0 -->
-<g id="edge3" class="edge">
+<g id="edge7" class="edge">
<title>7->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M815.97,-143.87C756.75,-116.48 641.43,-63.14 582.53,-35.9"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="583.78,-32.62 573.24,-31.6 580.84,-38.97 583.78,-32.62"/>
@@ -102,11 +102,11 @@
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M1123,-180C1123,-180 977,-180 977,-180 971,-180 965,-174 965,-168 965,-168 965,-156 965,-156 965,-150 971,-144 977,-144 977,-144 1123,-144 1123,-144 1129,-144 1135,-150 1135,-156 1135,-156 1135,-168 1135,-168 1135,-174 1129,-180 1123,-180"/>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1123,-180C1123,-180 977,-180 977,-180 971,-180 965,-174 965,-168 965,-168 965,-156 965,-156 965,-150 971,-144 977,-144 977,-144 1123,-144 1123,-144 1129,-144 1135,-150 1135,-156 1135,-156 1135,-168 1135,-168 1135,-174 1129,-180 1123,-180"/>
<text text-anchor="middle" x="1050" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 8->0 -->
-<g id="edge8" class="edge">
+<g id="edge1" class="edge">
<title>8->0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M989.46,-143.94C883.9,-114.2 669.21,-53.71 583.03,-29.43"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="583.74,-26 573.17,-26.65 581.84,-32.74 583.74,-26"/>
@@ -114,7 +114,7 @@
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M300.5,-180C300.5,-180 199.5,-180 199.5,-180 193.5,-180 187.5,-174 187.5,-168 187.5,-168 187.5,-156 187.5,-156 187.5,-150 193.5,-144 199.5,-144 199.5,-144 300.5,-144 300.5,-144 306.5,-144 312.5,-150 312.5,-156 312.5,-156 312.5,-168 312.5,-168 312.5,-174 306.5,-180 300.5,-180"/>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M300.5,-180C300.5,-180 199.5,-180 199.5,-180 193.5,-180 187.5,-174 187.5,-168 187.5,-168 187.5,-156 187.5,-156 187.5,-150 193.5,-144 199.5,-144 199.5,-144 300.5,-144 300.5,-144 306.5,-144 312.5,-150 312.5,-156 312.5,-156 312.5,-168 312.5,-168 312.5,-174 306.5,-180 300.5,-180"/>
<text text-anchor="middle" x="250" y="-159.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 9->3 -->
@@ -126,7 +126,7 @@
<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M425.5,-180C425.5,-180 342.5,-180 342.5,-180 336.5,-180 330.5,-174 330.5,-168 330.5,-168 330.5,-156 330.5,-156 330.5,-150 336.5,-144 342.5,-144 342.5,-144 425.5,-144 425.5,-144 431.5,-144 437.5,-150 437.5,-156 437.5,-156 437.5,-168 437.5,-168 437.5,-174 431.5,-180 425.5,-180"/>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M425.5,-180C425.5,-180 342.5,-180 342.5,-180 336.5,-180 330.5,-174 330.5,-168 330.5,-168 330.5,-156 330.5,-156 330.5,-150 336.5,-144 342.5,-144 342.5,-144 425.5,-144 425.5,-144 431.5,-144 437.5,-150 437.5,-156 437.5,-156 437.5,-168 437.5,-168 437.5,-174 431.5,-180 425.5,-180"/>
<text text-anchor="middle" x="384" y="-159.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 10->4 -->
@@ -138,23 +138,23 @@
<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M528,-252C528,-252 400,-252 400,-252 394,-252 388,-246 388,-240 388,-240 388,-228 388,-228 388,-222 394,-216 400,-216 400,-216 528,-216 528,-216 534,-216 540,-222 540,-228 540,-228 540,-240 540,-240 540,-246 534,-252 528,-252"/>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M528,-252C528,-252 400,-252 400,-252 394,-252 388,-246 388,-240 388,-240 388,-228 388,-228 388,-222 394,-216 400,-216 400,-216 528,-216 528,-216 534,-216 540,-222 540,-228 540,-228 540,-240 540,-240 540,-246 534,-252 528,-252"/>
<text text-anchor="middle" x="464" y="-231.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 11->5 -->
-<g id="edge12" class="edge">
+<g id="edge11" class="edge">
<title>11->5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M479.57,-215.7C487.2,-207.22 496.52,-196.86 504.88,-187.58"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="507.52,-189.88 511.61,-180.1 502.31,-185.2 507.52,-189.88"/>
</g>
<!-- 11->7 -->
-<g id="edge16" class="edge">
+<g id="edge15" class="edge">
<title>11->7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M540.44,-217.62C543.33,-217.07 546.19,-216.53 549,-216 615.58,-203.54 690.55,-190.46 749.38,-180.41"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="750.15,-183.83 759.42,-178.7 748.97,-176.93 750.15,-183.83"/>
</g>
<!-- 11->9 -->
-<g id="edge20" class="edge">
+<g id="edge19" class="edge">
<title>11->9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M411.92,-215.97C381.76,-206.1 343.61,-193.62 311.92,-183.25"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="312.9,-179.89 302.31,-180.11 310.73,-186.55 312.9,-179.89"/>
@@ -162,17 +162,17 @@
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<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M667.5,-252C667.5,-252 570.5,-252 570.5,-252 564.5,-252 558.5,-246 558.5,-240 558.5,-240 558.5,-228 558.5,-228 558.5,-222 564.5,-216 570.5,-216 570.5,-216 667.5,-216 667.5,-216 673.5,-216 679.5,-222 679.5,-228 679.5,-228 679.5,-240 679.5,-240 679.5,-246 673.5,-252 667.5,-252"/>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M667.5,-252C667.5,-252 570.5,-252 570.5,-252 564.5,-252 558.5,-246 558.5,-240 558.5,-240 558.5,-228 558.5,-228 558.5,-222 564.5,-216 570.5,-216 570.5,-216 667.5,-216 667.5,-216 673.5,-216 679.5,-222 679.5,-228 679.5,-228 679.5,-240 679.5,-240 679.5,-246 673.5,-252 667.5,-252"/>
<text text-anchor="middle" x="619" y="-231.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 12->5 -->
-<g id="edge11" class="edge">
+<g id="edge12" class="edge">
<title>12->5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M596.26,-215.7C584.56,-206.8 570.14,-195.82 557.49,-186.2"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="559.56,-183.37 549.48,-180.1 555.32,-188.94 559.56,-183.37"/>
</g>
<!-- 12->6 -->
-<g id="edge13" class="edge">
+<g id="edge14" class="edge">
<title>12->6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M633.83,-215.7C641.02,-207.3 649.8,-197.07 657.69,-187.86"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="660.49,-189.97 664.34,-180.1 655.17,-185.42 660.49,-189.97"/>
@@ -180,23 +180,23 @@
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M820,-252C820,-252 710,-252 710,-252 704,-252 698,-246 698,-240 698,-240 698,-228 698,-228 698,-222 704,-216 710,-216 710,-216 820,-216 820,-216 826,-216 832,-222 832,-228 832,-228 832,-240 832,-240 832,-246 826,-252 820,-252"/>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M820,-252C820,-252 710,-252 710,-252 704,-252 698,-246 698,-240 698,-240 698,-228 698,-228 698,-222 704,-216 710,-216 710,-216 820,-216 820,-216 826,-216 832,-222 832,-228 832,-228 832,-240 832,-240 832,-246 826,-252 820,-252"/>
<text text-anchor="middle" x="765" y="-231.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 13->6 -->
-<g id="edge14" class="edge">
+<g id="edge13" class="edge">
<title>13->6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M743.74,-215.7C732.91,-206.88 719.58,-196.03 707.84,-186.47"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="709.98,-183.7 700.01,-180.1 705.56,-189.13 709.98,-183.7"/>
</g>
<!-- 13->8 -->
-<g id="edge18" class="edge">
+<g id="edge17" class="edge">
<title>13->8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M832.18,-216.5C873.55,-206.34 926.82,-193.26 970.32,-182.57"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="971.42,-185.9 980.29,-180.12 969.75,-179.11 971.42,-185.9"/>
</g>
<!-- 13->10 -->
-<g id="edge22" class="edge">
+<g id="edge21" class="edge">
<title>13->10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M697.86,-217.89C694.53,-217.23 691.23,-216.6 688,-216 584.62,-196.89 554.75,-201.82 447.45,-179.95"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="448.02,-176.49 437.52,-177.89 446.6,-183.35 448.02,-176.49"/>
@@ -204,17 +204,17 @@
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M961.5,-252C961.5,-252 864.5,-252 864.5,-252 858.5,-252 852.5,-246 852.5,-240 852.5,-240 852.5,-228 852.5,-228 852.5,-222 858.5,-216 864.5,-216 864.5,-216 961.5,-216 961.5,-216 967.5,-216 973.5,-222 973.5,-228 973.5,-228 973.5,-240 973.5,-240 973.5,-246 967.5,-252 961.5,-252"/>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M961.5,-252C961.5,-252 864.5,-252 864.5,-252 858.5,-252 852.5,-246 852.5,-240 852.5,-240 852.5,-228 852.5,-228 852.5,-222 858.5,-216 864.5,-216 864.5,-216 961.5,-216 961.5,-216 967.5,-216 973.5,-222 973.5,-228 973.5,-228 973.5,-240 973.5,-240 973.5,-246 967.5,-252 961.5,-252"/>
<text text-anchor="middle" x="913" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 14->7 -->
-<g id="edge15" class="edge">
+<g id="edge16" class="edge">
<title>14->7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M898.17,-215.7C890.98,-207.3 882.2,-197.07 874.31,-187.86"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="876.83,-185.42 867.66,-180.1 871.51,-189.97 876.83,-185.42"/>
</g>
<!-- 14->8 -->
-<g id="edge17" class="edge">
+<g id="edge18" class="edge">
<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 6f043f8..0000000
--- 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 f0f0eba..d39db9c 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 0000000..7697b12
--- /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 0000000..cc0ec82
--- /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 f838343..47335f6 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 de4b713..7e09a2d 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 e372afb..0000000
--- 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 e1d111b..0000000
--- 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 7c6b040..0000000
--- 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 e41d542..0000000
--- 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 a55426c..0000000
--- 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
GIT binary patch
literal 0
HcmV?d00001
literal 713
zcmb2|=HS?*=n%)iTwIw~l95`HnXH$aSdtoVsF#*lTvEuebn4l>+XezH@9VmlY@az8
zmSsdfP>goE!Ngjm$$$3uevkAt)thdQ<rj4Me$+o!H|OTl-^br?PrUKGQ0jEuub)4E
zz5d+(KQnk<(K+T@&X$X0PkoG@XSXb|X!E_<-^KISZqKW|e!<YZclOK6Qpc`cJeu~#
zX?d}1e|hO_%kUkt`(ONET=zb%?Bs`<?LXfo$81ju6P{%$nU>|bRLm^Q&`0&{J^2HB
z<@kOJKRh<Ophq;Ljo~6|LV5TF*&4MlmviDLldjGxzS8={rv2Pw#yOmP3)zp>{G9cC
z%7>MlEI%Ig*UnDvOR0JkDu4Lt;gx#?-<3pLu5`RAVs%ZzD5*5C`u3L3KjfdU5!<17
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zmM!_zz?q~v{dCtxvFI7oa(4UF=AJf4j*`vF+^nIH;l<!&xj1t51rG5;fd|?P+9&a+
zoGx#1PWyQ0@QhVLBFApCZCo<#gAaG_+8sFukDZL!aPv>8XJ-ymV3bDKq@Y*Rvi~?;
zZ_iQgQoZ@@dQM%WwrXSqZz#X>?JTwEc<bjUm%j0MrVy?x6dh^Qmzos%o=YUr`2K|C
znn_xVMJCViw$=1ciIMY9RfyTC8`E;~kKxjQE27;(7i(W``5<SxKvsQb``u}tXJcYm
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cOG14Ev({V_=ofE(cKV(E%NjMm`5X)k0B4j}-2eap
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
GIT binary patch
literal 0
HcmV?d00001
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zcmb2|=HPgs=n%)iTwIw~l95`HnXH$aSdtoVq?eXhTvEuebn3yp+XezI@Bei%**<f)
zSe6m_KvCK$p^<543IEyu|2@*vRBtmTopwmAbX}X#>~Flg=J$`!Ry^%Ce#w?T`|ZB(
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diff --git a/tests/test_create_dag_image/samples.tsv b/tests/test_create_dag_image/samples.tsv
deleted file mode 100644
index 3793d81..0000000
--- 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 c377a7e..67bf41c 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 e1d111b..0000000
--- 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 7c6b040..0000000
--- 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 e41d542..0000000
--- 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 a55426c..0000000
--- 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
GIT binary patch
literal 0
HcmV?d00001
literal 713
zcmb2|=HS?*=n%)iTwIw~l95`HnXH$aSdtoVsF#*lTvEuebn4l>+XezH@9VmlY@az8
zmSsdfP>goE!Ngjm$$$3uevkAt)thdQ<rj4Me$+o!H|OTl-^br?PrUKGQ0jEuub)4E
zz5d+(KQnk<(K+T@&X$X0PkoG@XSXb|X!E_<-^KISZqKW|e!<YZclOK6Qpc`cJeu~#
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zZ_iQgQoZ@@dQM%WwrXSqZz#X>?JTwEc<bjUm%j0MrVy?x6dh^Qmzos%o=YUr`2K|C
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cOG14Ev({V_=ofE(cKV(E%NjMm`5X)k0B4j}-2eap
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
GIT binary patch
literal 0
HcmV?d00001
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zcmb2|=HPgs=n%)iTwIw~l95`HnXH$aSdtoVq?eXhTvEuebn3yp+XezI@Bei%**<f)
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diff --git a/tests/test_create_rule_graph/samples.tsv b/tests/test_create_rule_graph/samples.tsv
deleted file mode 100644
index 3793d81..0000000
--- 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 b67a888..00637f5 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 e1d111b..0000000
--- 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 61c6178..a60f623 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -1,132 +1,87 @@
-results/homo_sapiens/kallisto.idx
-results/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
-results/homo_sapiens/31/salmon.idx/hash.bin
-results/homo_sapiens/31/salmon.idx/header.json
-results/homo_sapiens/31/salmon.idx/refInfo.json
-results/homo_sapiens/31/salmon.idx/rsd.bin
-results/homo_sapiens/31/salmon.idx/sa.bin
-results/homo_sapiens/31/salmon.idx/txpInfo.bin
-results/homo_sapiens/31/salmon.idx/versionInfo.json
-results/homo_sapiens/76/STAR_index/chrLength.txt
-results/homo_sapiens/76/STAR_index/chrNameLength.txt
-results/homo_sapiens/76/STAR_index/chrName.txt
-results/homo_sapiens/76/STAR_index/chrStart.txt
-results/homo_sapiens/76/STAR_index/exonGeTrInfo.tab
-results/homo_sapiens/76/STAR_index/exonInfo.tab
-results/homo_sapiens/76/STAR_index/geneInfo.tab
-results/homo_sapiens/76/STAR_index/Genome
-results/homo_sapiens/76/STAR_index/genomeParameters.txt
-results/homo_sapiens/76/STAR_index/SA
-results/homo_sapiens/76/STAR_index/SAindex
-results/homo_sapiens/76/STAR_index/sjdbInfo.txt
-results/homo_sapiens/76/STAR_index/sjdbList.fromGTF.out.tab
-results/homo_sapiens/76/STAR_index/sjdbList.out.tab
-results/homo_sapiens/76/STAR_index/transcriptInfo.tab
-results/paired_end/synthetic_10_reads_paired/synthetic_10_reads_paired.remove_adapters_mate1.fastq
-results/paired_end/synthetic_10_reads_paired/synthetic_10_reads_paired.remove_adapters_mate2.fastq
-results/paired_end/synthetic_10_reads_paired/synthetic_10_reads_paired.remove_polya_mate1.fastq
-results/paired_end/synthetic_10_reads_paired/synthetic_10_reads_paired.remove_polya_mate2.fastq
-results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam
-results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam.bai
-results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_SJ.out.tab
-results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired__STARgenome/sjdbInfo.txt
-results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired__STARgenome/sjdbList.out.tab
-results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired__STARpass1/SJ.out.tab
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_sequence_content.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_gc_content.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_tile_quality.png
-results/paired_end/synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/sequence_length_distribution.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc_data.txt
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc.fo
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/summary.txt
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/adapter_content.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/duplication_levels.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_n_content.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_quality.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_sequence_content.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_gc_content.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_quality.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_tile_quality.png
-results/paired_end/synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/sequence_length_distribution.png
-results/paired_end/synthetic_10_reads_paired/quant_kallisto/abundance.tsv
-results/paired_end/synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
-results/paired_end/synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired.kallisto.pseudo.sam
-results/paired_end/synthetic_10_reads_paired/salmon_quant/cmd_info.json
-results/paired_end/synthetic_10_reads_paired/salmon_quant/lib_format_counts.json
-results/paired_end/synthetic_10_reads_paired/salmon_quant/aux_info/ambig_info.tsv
-results/paired_end/synthetic_10_reads_paired/salmon_quant/aux_info/expected_bias
-results/paired_end/synthetic_10_reads_paired/salmon_quant/aux_info/observed_bias
-results/paired_end/synthetic_10_reads_paired/salmon_quant/aux_info/observed_bias_3p
-results/paired_end/synthetic_10_reads_paired/salmon_quant/aux_info/unmapped_names.txt
-results/single_end/synthetic_10_reads_mate_1/synthetic_10_reads_mate_1.remove_adapters_mate1.fastq
-results/single_end/synthetic_10_reads_mate_1/synthetic_10_reads_mate_1.remove_polya_mate1.fastq
-results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam
-results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam.bai
-results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_SJ.out.tab
-results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1__STARgenome/sjdbInfo.txt
-results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1__STARgenome/sjdbList.out.tab
-results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1__STARpass1/SJ.out.tab
-results/single_end/synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
-results/single_end/synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
-results/single_end/synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 4ac2dc9..01c8966 100644
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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 7c6b040..0000000
--- a/tests/test_integration_workflow/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_integration_workflow/input_files/chr1-10000-20000.gtf b/tests/test_integration_workflow/input_files/chr1-10000-20000.gtf
deleted file mode 100644
index e41d542..0000000
--- 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 a55426c..0000000
--- 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 47335f6..0000000
--- 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
GIT binary patch
literal 0
HcmV?d00001
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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 7e09a2d..0000000
--- a/tests/test_integration_workflow/input_files/synthetic.mate_2.bed
+++ /dev/null
@@ -1,10 +0,0 @@
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-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
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-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
GIT binary patch
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zTz^fpxy5!Whfyuq>-ra#7|Hn0$!6ig2PJ>cSyH4Mb6PxQ$;)#ZhTAI?SFaP<_WgG4
zgG;vS%Jyg-HwxZ8MR2S2mDS3ZlkTd2YrO1O@ZEgpfBh}XCVkC+@b2vsH>u3f;4M<C
XO^-Z2wxH(bU*?HhgkH_(U|;|MK`2YM
diff --git a/tests/test_integration_workflow/samples.tsv b/tests/test_integration_workflow/samples.tsv
deleted file mode 100644
index 0d242e0..0000000
--- 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 a87ff58..32923b4 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 246a1e5..7f773ee 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 9f6d770..1dcb38f 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 f688762..0000000
--- 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 a62b53b..c9d1a27 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 0000000..1dcb38f
--- /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 0000000..ee6d5fc
--- /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 0000000..63632e0
--- /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
--
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