chore: Change Oncoliner to ONCOLINER

EUCANCan · Oct 17, 2023 · 728dc3a · 728dc3a
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-# Oncoliner<!-- omit in toc -->
+# ONCOLINER<!-- omit in toc -->
 
-![Oncoliner logo](/docs/images/ONCOLINER_LOGO_COLOR.png)
+![ONCOLINER logo](/docs/images/ONCOLINER_LOGO_COLOR.png)
 
 WIP
 
@@ -18,7 +18,7 @@ WIP
 
 ## Installation
 
-It is highly recommended to use Oncoliner with Docker or Singularity (we recommend using [`singularity-ce`](https://github.com/sylabs/singularity) with a version higher than 3.9.0). However, you may also install it locally.
+It is highly recommended to use ONCOLINER with Docker or Singularity (we recommend using [`singularity-ce`](https://github.com/sylabs/singularity) with a version higher than 3.9.0). However, you may also install it locally.
 
 ### Docker / Singularity
 
@@ -34,11 +34,11 @@ singularity build oncoliner.sif singularity.def
 
 ### Local installation
 
-You may also install Oncoliner locally using the same instructions as provided in the [Dockerfile](/Dockerfile).
+You may also install ONCOLINER locally using the same instructions as provided in the [Dockerfile](/Dockerfile).
 
 ## Usage
 
-Assuming you have a singularity image called `oncoliner.sif`, you can run Oncoliner as follows:
+Assuming you have a singularity image called `oncoliner.sif`, you can run ONCOLINER as follows:
 
 ```bash
 singularity exec oncoliner.sif oncoliner/main.py -c config.tsv -pf pipelines_1_folder pipelines_2_folder -o output_folder --max-processes 48
@@ -48,7 +48,7 @@ singularity exec oncoliner.sif oncoliner/main.py -c config.tsv -pf pipelines_1_f
 ```
 usage: main.py [-h] -c CONFIG -pf PIPELINES_FOLDERS [PIPELINES_FOLDERS ...] -o OUTPUT [-cf CALLERS_FOLDER] [--max-processes MAX_PROCESSES]
 
-Oncoliner
+ONCOLINER
 
 options:
   -h, --help            show this help message and exit
@@ -80,11 +80,11 @@ You can check an example of configuration file in [`example/example_config.tsv`]
 
 ### Normalization
 
-It is recommended to normalize indels and SNVs before executing Oncoliner. For this purpose, we recommend using pre.py from [Illumina's Haplotype Comparison Tools (hap.py)](https://github.com/Illumina/hap.py). We provide an standalone and containerized **[EUCANCan's pre.py wrapper](https://github.com/EUCANCan/prepy-wrapper)** for this purpose, specially the bulk version of the wrapper. You can check an example of usage in [`example/example_prepy.sh`](/example/example_prepy.sh).
+It is recommended to normalize indels and SNVs before executing ONCOLINER. For this purpose, we recommend using pre.py from [Illumina's Haplotype Comparison Tools (hap.py)](https://github.com/Illumina/hap.py). We provide an standalone and containerized **[EUCANCan's pre.py wrapper](https://github.com/EUCANCan/prepy-wrapper)** for this purpose, specially the bulk version of the wrapper. You can check an example of usage in [`example/example_prepy.sh`](/example/example_prepy.sh).
 
 ## Tools
 
-Along with Oncoliner, in this repository you can find some tools that may be useful.
+Along with ONCOLINER, in this repository you can find some tools that may be useful.
 
 ### Pipeline designer
 
@@ -96,7 +96,7 @@ WIP
 
 ## Modularity
 
-Oncoliner is divided into three functional modules (assesment, improvement and harmonization) and a UI module. For more information about each module, check the corresponding README file in the [`modules`](/modules) folder:
+ONCOLINER is divided into three functional modules (assesment, improvement and harmonization) and a UI module. For more information about each module, check the corresponding README file in the [`modules`](/modules) folder:
 
 * [Assesment README](/modules/oncoliner_assesment/README.md)
 * [Improvement README](/modules/oncoliner_improvement/README.md)

diff --git a/modules/oncoliner_assesment/README.md b/modules/oncoliner_assesment/README.md
@@ -1,6 +1,6 @@
-# Oncoliner: Assesment module<!-- omit in toc -->
+# ONCOLINER: Assesment module<!-- omit in toc -->
 
-![Oncoliner logo](../../docs/images/ONCOLINER_LOGO_COLOR.png)
+![ONCOLINER logo](../../docs/images/ONCOLINER_LOGO_COLOR.png)
 
 Evaluator of variants (SNVs, indels and SVs) from test VCFs against truth VCFs. It is provided as a standalone command line tool to allow for the comparison of a series of (VCF/BCF/VCF.GZ) files generated by any variant callers against a series of (VCF/BCF/VCF.GZ) truth files. If provided in the truth files the module will also provide information about the genes affected by the variants. Check the [Functional analysis](#functional-analysis) section for more information.
 
@@ -17,7 +17,7 @@ It is written in Python 3 (**requires Python version 3.6 or higher**).
     - [Configuration file](#configuration-file)
 
 ## Dependencies
-Oncoliner's assesment module makes use of the following Python modules:
+ONCOLINER's assesment module makes use of the following Python modules:
 * [`pandas`](https://pandas.pydata.org/)
 * [`pysam`](https://github.com/pysam-developers/pysam)
 * [`variant-extractor`](https://github.com/EUCANCan/variant-extractor)
@@ -27,12 +27,12 @@ You may install them using pip:
 pip3 install pandas pysam variant-extractor
 ```
 
-However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole Oncoliner suite to avoid dependency issues.
+However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole ONCOLINER suite to avoid dependency issues.
 
 ## Functional analysis
 
-The module will try to obtain the genes affected by the variants from the `INFO` field in the truth files. **WARNING: Oncoliner does not compute genes linked to false positives.** Oncoliner's assesment module is compatible with the following functional analysis tools annotations:
-* Oncoliner.
+The module will try to obtain the genes affected by the variants from the `INFO` field in the truth files. **WARNING: ONCOLINER does not compute genes linked to false positives.** ONCOLINER's assesment module is compatible with the following functional analysis tools annotations:
+* ONCOLINER.
 * [**VEP**](https://www.ensembl.org/info/docs/tools/vep/index.html): Variant Effect Predictor from Ensembl.
 
 
@@ -60,7 +60,7 @@ Check the example of usage in [`example/example_main.sh`](./example/example_main
 usage: assesment_main.py [-h] -t TRUTHS [TRUTHS ...] -v TESTS [TESTS ...] -o OUTPUT_PREFIX -f FASTA_REF [-it INDEL_THRESHOLD] [-wr WINDOW_RADIUS] [--sv-size-bins SV_SIZE_BINS [SV_SIZE_BINS ...]]
                          [--contigs CONTIGS [CONTIGS ...]] [--keep-intermediates] [--no-gzip]
 
-Oncoliner Assesment
+ONCOLINER Assesment
 
 options:
   -h, --help            show this help message and exit
@@ -129,7 +129,7 @@ The configuration file is a TSV file with the following columns:
 usage: assesment_bulk.py [-h] -c CONFIG_FILE -o OUTPUT_FOLDER [-it INDEL_THRESHOLD] [-wr WINDOW_RADIUS] [--sv-size-bins SV_SIZE_BINS [SV_SIZE_BINS ...]] [--contigs CONTIGS [CONTIGS ...]] [--keep-intermediates]
                          [--no-gzip] [-p MAX_PROCESSES]
 
-Oncoliner Assesment Bulk
+ONCOLINER Assesment Bulk
 
 options:
   -h, --help            show this help message and exit

diff --git a/modules/oncoliner_assesment/src/assesment_bulk.py b/modules/oncoliner_assesment/src/assesment_bulk.py
@@ -65,7 +65,7 @@ def aggregate_metrics_from_samples(output_file: str, samples_folder: str, recall
 
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Oncoliner Assesment Bulk')
+    parser = argparse.ArgumentParser(description='ONCOLINER Assesment Bulk')
     parser.add_argument('-c', '--config-file', required=True, type=str, help='Path to the config TSV file')
     parser.add_argument('-o', '--output-folder', required=True, type=str, help='Path to the output folder')
     parser.add_argument('-it', '--indel-threshold',

diff --git a/modules/oncoliner_assesment/src/assesment_main.py b/modules/oncoliner_assesment/src/assesment_main.py
@@ -130,7 +130,7 @@ def main(truth_vcfs, test_vcfs, output_prefix, fasta_ref, indel_threshold=DEFAUL
 
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Oncoliner Assesment')
+    parser = argparse.ArgumentParser(description='ONCOLINER Assesment')
     parser.add_argument('-t', '--truths', help='Path to the VCF truth files', nargs='+', required=True, type=str)
     parser.add_argument('-v', '--tests', help='Path to the VCF test files', nargs='+', required=True, type=str)
     parser.add_argument('-o', '--output_prefix',

diff --git a/modules/oncoliner_harmonization/README.md b/modules/oncoliner_harmonization/README.md
@@ -1,11 +1,11 @@
-# Oncoliner: Harmonization module<!-- omit in toc -->
+# ONCOLINER: Harmonization module<!-- omit in toc -->
 
-![Oncoliner logo](../../docs/images/ONCOLINER_LOGO_COLOR.png)
+![ONCOLINER logo](../../docs/images/ONCOLINER_LOGO_COLOR.png)
 
 WIP
 
 ## Dependencies
-Oncoliner's harmonization module makes use of the following Python modules:
+ONCOLINER's harmonization module makes use of the following Python modules:
 * [`pandas`](https://pandas.pydata.org/)
 * [`pysam`](https://github.com/pysam-developers/pysam)
 * [`variant-extractor`](https://github.com/EUCANCan/variant-extractor)
@@ -15,4 +15,4 @@ You may install them using pip:
 pip3 install pandas pysam variant-extractor
 ```
 
-However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole Oncoliner suite to avoid dependency issues.
+However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole ONCOLINER suite to avoid dependency issues.
diff --git a/modules/oncoliner_improvement/README.md b/modules/oncoliner_improvement/README.md
@@ -1,6 +1,6 @@
-# Oncoliner: Improvement module <!-- omit in toc -->
+# ONCOLINER: Improvement module <!-- omit in toc -->
 
-![Oncoliner logo](../../docs/images/ONCOLINER_LOGO_COLOR.png)
+![ONCOLINER logo](../../docs/images/ONCOLINER_LOGO_COLOR.png)
 
 WIP
 
@@ -11,7 +11,7 @@ WIP
 
 
 ## Dependencies
-Oncoliner's improvement module makes use of the following Python modules:
+ONCOLINER's improvement module makes use of the following Python modules:
 * [`pandas`](https://pandas.pydata.org/)
 * [`pysam`](https://github.com/pysam-developers/pysam)
 * [`variant-extractor`](https://github.com/EUCANCan/variant-extractor)
@@ -21,14 +21,14 @@ You may install them using pip:
 pip3 install pandas pysam variant-extractor
 ```
 
-However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole Oncoliner suite to avoid dependency issues.
+However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole ONCOLINER suite to avoid dependency issues.
 
 
 ## Usage
 ```
 usage: main.py [-h] -e EVALUATION_RESULTS -c CALLERS_FOLDER -o OUTPUT -rs RECALL_SAMPLES [RECALL_SAMPLES ...] -ps PRECISION_SAMPLES [PRECISION_SAMPLES ...] [-lm LOSS_MARGIN] [-wr WINDOW_RADIUS] [-p PROCESSES]
 
-Oncoliner Improvement
+ONCOLINER Improvement
 
 options:
   -h, --help            show this help message and exit

diff --git a/modules/oncoliner_improvement/src/improvement_main.py b/modules/oncoliner_improvement/src/improvement_main.py
@@ -3,7 +3,7 @@
 from _internal.recommendator import main
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Oncoliner Improvement')
+    parser = argparse.ArgumentParser(description='ONCOLINER Improvement')
     parser.add_argument('-e', '--evaluation-results', type=str, required=True,
                         help='Pipeline evaluation results folder path')
     parser.add_argument('-c', '--callers-folder', type=str, required=True, help='Callers folder path')

diff --git a/modules/oncoliner_ui/src/ui/html_templates/conf.json b/modules/oncoliner_ui/src/ui/html_templates/conf.json
@@ -98,13 +98,13 @@
       "protein_affected_genes":{
          "name":"Prot. genes",
          "tooltip":"Genes whose proteins are affected by discovered variants (only TP)",
-         "legend": "Warning: Oncoliner does not compute genes linked to false positives.",
+         "legend": "Warning: ONCOLINER does not compute genes linked to false positives.",
          "sortable": true
       },
       "protein_affected_driver_genes":{
          "name":"Cancer driver prot. genes",
          "tooltip":"Cancer driver genes whose proteins are affected by discovered variants (only TP)",
-         "legend": "Warning: Oncoliner does not compute genes linked to false positives.",
+         "legend": "Warning: ONCOLINER does not compute genes linked to false positives.",
          "sortable": true
       },
       "added_callers":{

diff --git a/modules/oncoliner_ui/src/ui/html_templates/index/base.html b/modules/oncoliner_ui/src/ui/html_templates/index/base.html
@@ -4,8 +4,8 @@
         <meta charset="utf-8">
         <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
         <meta name="theme-color" content="#33b5e5">
-        <title>Oncoliner report</title>
-        <link rel="shortcut icon" href="data:image/svg+xml,{{ include_encoded('index/svg/Oncoliner_icon.svg') }}" >
+        <title>ONCOLINER report</title>
+        <link rel="shortcut icon" href="data:image/svg+xml,{{ include_encoded('index/svg/ONCOLINER_icon.svg') }}" >
         {% block styles %}
         <style type="text/css">{{ include_raw('index/css_external/[email protected]/bootstrap.min.css') }}</style>
         <style type="text/css">{{ include_raw('index/css_external/[email protected]/datatables.min.css') }}</style>
@@ -54,7 +54,7 @@
 
         <!-- TODO: Henri: The "fade" class does not work, no animation is shown -->
         <section role="tabpanel">
-            <div id="main-oncoliner-logo" class="logo-container"> {{include_raw('index/svg/Oncoliner_logo.svg')}} </div>
+            <div id="main-oncoliner-logo" class="logo-container"> {{include_raw('index/svg/ONCOLINER_logo.svg')}} </div>
             <nav class="nav nav-tabs main-nav-tabs">
                 <div class="nav viz-nav-tabs-container" id="nav-tab" role="tablist">
                     <button class="nav-link active" id="nav-assesment-tab" data-bs-toggle="tab" data-bs-target="#nav-assesment" type="button" role="tab" aria-controls="nav-assesment" aria-selected="true">Assesment</button>
@@ -83,7 +83,7 @@
         <footer class="viz-footer">
             <div>
                 <p>
-                    Report generated by <a href="{{conf['commons']['links']['oncoliner']}}" target="_blank">Oncoliner</a>.
+                    Report generated by <a href="{{conf['commons']['links']['oncoliner']}}" target="_blank">ONCOLINER</a>.
                 </p>
                 <p>
                     This report uses

diff --git a/...ml_templates/index/svg/Oncoliner_icon.svg → ...ml_templates/index/svg/ONCOLINER_icon.svg b/...ml_templates/index/svg/Oncoliner_icon.svg → ...ml_templates/index/svg/ONCOLINER_icon.svg
diff --git a/...ml_templates/index/svg/Oncoliner_logo.svg → ...ml_templates/index/svg/ONCOLINER_logo.svg b/...ml_templates/index/svg/Oncoliner_logo.svg → ...ml_templates/index/svg/ONCOLINER_logo.svg
diff --git a/modules/oncoliner_ui/src/ui/html_templates/shared/warning_panel.html b/modules/oncoliner_ui/src/ui/html_templates/shared/warning_panel.html
@@ -18,5 +18,5 @@
         {% endif %}
     </div>
     {% endfor %}
-    <p>If any of these warnings are relevant to your analysis, please check the configuration file and input VCF files and execute Oncoliner again.</p>
+    <p>If any of these warnings are relevant to your analysis, please check the configuration file and input VCF files and execute ONCOLINER again.</p>
 </div>
diff --git a/oncoliner_launcher.py b/oncoliner_launcher.py
@@ -99,7 +99,7 @@ def check_samples_folders(pipeline_folder_path: str, sample_names: Set[str]) ->
 
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Oncoliner')
+    parser = argparse.ArgumentParser(description='ONCOLINER')
     parser.add_argument('-c', '--config', type=str, required=True, help='Path to config file')
     parser.add_argument('-pf', '--pipelines-folders', type=str, required=True, nargs='+', help='Paths to pipelines folders')
     parser.add_argument('-o', '--output', type=str, required=True, help='Path to output folder')
@@ -173,4 +173,4 @@ def check_samples_folders(pipeline_folder_path: str, sample_names: Set[str]) ->
     run_ui(pipelines_evaluation_folder_paths, pipeline_improvements_folder_paths,
            args.callers_folder, output_harmonization_folder, ui_output_file)
 
-    logging.info(f'Oncoliner report available at {ui_output_file}')
+    logging.info(f'ONCOLINER report available at {ui_output_file}')
diff --git a/tools/pipeline_designer/README.md b/tools/pipeline_designer/README.md
@@ -1,10 +1,10 @@
 # Pipeline Designer<!-- omit in toc -->
 
-Pipeline Designer is a standalone tool that allows the user to combine the results of different variant callers to improve the results of a variant calling pipeline. Pipeline Designer outputs the list of the best combinations of variant callers for each variant type and size, including SNVs, indels and SVs. Pipeline Designer also displays the F1-score, precision, recall and the number and names of genes discovered (if provided) of each combination (see [Oncoliner's assesment module](../../modules/oncoliner_assesment/) for more information about the evaluation process).
+Pipeline Designer is a standalone tool that allows the user to combine the results of different variant callers to improve the results of a variant calling pipeline. Pipeline Designer outputs the list of the best combinations of variant callers for each variant type and size, including SNVs, indels and SVs. Pipeline Designer also displays the F1-score, precision, recall and the number and names of genes discovered (if provided) of each combination (see [ONCOLINER's assesment module](../../modules/oncoliner_assesment/) for more information about the evaluation process).
 
 The user just needs to provide the VCF files of the variant callers they want to combine as well as the truth files of the samples. The user must also specify which samples should be used to compute recall related metrics and which samples should be used to compute precision related metrics. Pipeline Designer will automatically combine the variant callers and evaluate the results. Check the [Use case example](#use-case-example) section for more information.
 
-Pipeline Designer is part of the [Oncoliner suite](../../README.md) and is provided as a standalone command line tool. It is available as in the [Docker image](../../Dockerfile) and [Singularity image](../../singularity.def) of Oncoliner.
+Pipeline Designer is part of the [ONCOLINER suite](../../README.md) and is provided as a standalone command line tool. It is available as in the [Docker image](../../Dockerfile) and [Singularity image](../../singularity.def) of ONCOLINER.
 
 ## Table of contents<!-- omit in toc -->
 - [Dependencies](#dependencies)
@@ -15,7 +15,7 @@ Pipeline Designer is part of the [Oncoliner suite](../../README.md) and is provi
 
 
 ## Dependencies
-Oncoliner's pipeline designer makes use of the following Python modules:
+ONCOLINER's pipeline designer makes use of the following Python modules:
 * [`pandas`](https://pandas.pydata.org/)
 * [`pysam`](https://github.com/pysam-developers/pysam)
 * [`pysam`](https://github.com/pysam-developers/pysam)
@@ -25,7 +25,7 @@ You may install them using pip:
 pip3 install pandas pysam variant-extractor
 ```
 
-However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole Oncoliner suite to avoid dependency issues.
+However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole ONCOLINER suite to avoid dependency issues.
 
 ## Usage