From 728dc3aebd40f9ba7ecfe1d2a75df56107cfff17 Mon Sep 17 00:00:00 2001 From: Rapsssito Date: Tue, 17 Oct 2023 10:08:20 +0200 Subject: [PATCH] chore: Change Oncoliner to ONCOLINER --- README.md | 18 +++++++++--------- modules/oncoliner_assesment/README.md | 16 ++++++++-------- .../oncoliner_assesment/src/assesment_bulk.py | 2 +- .../oncoliner_assesment/src/assesment_main.py | 2 +- modules/oncoliner_harmonization/README.md | 8 ++++---- modules/oncoliner_improvement/README.md | 10 +++++----- .../src/improvement_main.py | 2 +- .../src/ui/html_templates/conf.json | 4 ++-- .../src/ui/html_templates/index/base.html | 8 ++++---- .../{Oncoliner_icon.svg => ONCOLINER_icon.svg} | 0 .../{Oncoliner_logo.svg => ONCOLINER_logo.svg} | 0 .../html_templates/shared/warning_panel.html | 2 +- oncoliner_launcher.py | 4 ++-- tools/pipeline_designer/README.md | 8 ++++---- 14 files changed, 42 insertions(+), 42 deletions(-) rename modules/oncoliner_ui/src/ui/html_templates/index/svg/{Oncoliner_icon.svg => ONCOLINER_icon.svg} (100%) rename modules/oncoliner_ui/src/ui/html_templates/index/svg/{Oncoliner_logo.svg => ONCOLINER_logo.svg} (100%) diff --git a/README.md b/README.md index ee8bc92..bd08053 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# Oncoliner +# ONCOLINER -![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 index 6525526..516944b 100644 --- a/modules/oncoliner_assesment/README.md +++ b/modules/oncoliner_assesment/README.md @@ -1,6 +1,6 @@ -# Oncoliner: Assesment module +# ONCOLINER: Assesment module -![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 index 3eeb7b1..908f1f5 100644 --- 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 index 2b5cddf..7e271d8 100644 --- 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 index 88979c2..2bbb829 100644 --- a/modules/oncoliner_harmonization/README.md +++ b/modules/oncoliner_harmonization/README.md @@ -1,11 +1,11 @@ -# Oncoliner: Harmonization module +# ONCOLINER: Harmonization module -![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 index 6a0bd02..9055ed0 100644 --- a/modules/oncoliner_improvement/README.md +++ b/modules/oncoliner_improvement/README.md @@ -1,6 +1,6 @@ -# Oncoliner: Improvement module +# ONCOLINER: Improvement module -![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 index 6651389..638fba7 100644 --- 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 index ffc3884..e9a7cba 100644 --- 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 index 0a85b15..6a1144b 100644 --- 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 @@ - Oncoliner report - + ONCOLINER report + {% block styles %} @@ -54,7 +54,7 @@
- +