From c946ac0ac34b21ddcb5c871b22f3b11599be783d Mon Sep 17 00:00:00 2001
From: koszulordie <70538316+koszulordie@users.noreply.github.com>
Date: Wed, 20 Dec 2023 10:12:45 +0100
Subject: [PATCH] Create README.md

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+# boostDM-CH pipeline
+
+**BoostDM-CH** is a method to score all possible single base substitutions in clonal hematopoiesis (CH) driver genes for their potential to drive CH.
+
+The method's rationale and analysis results thereof are described in this study:
+
+**Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis**
+Santiago Demajo, Joan Enric Ramis-Zaldivar, Ferran Muiños, Miguel L Grau, Maria Andrianova, Nuria Lopez-Bigas, Abel Gonzalez-Perez
+medRxiv 2023.12.13.23299893 
+URL: [https://doi.org/10.1101/2023.12.13.23299893](https://doi.org/10.1101/2023.12.13.23299893)
+
+The method is based on two previous projects: **IntOGen-CH** and **boostDM**
+
+**IntOGen-CH** pipeline provides a compendium of CH driver genes and mutational features upon using the **IntOGen** pipeline with a catalog of high VAF somatic mutations called in normal blood from tumor samples by reverse variant calling, which has been described in this study:
+
+**Discovering the drivers of clonal hematopoiesis**
+Oriol Pich, Iker Reyes-Salazar, Abel Gonzalez-Perez, Nuria Lopez-Bigas 
+URL: [https://doi.org/10.1038/s41467-022-31878-0](https://doi.org/10.1038/s41467-022-31878-0)
+
+**boostDM** is a methodology to annotate mutations in cancer genes for their potential to drive tumorigenesis, which has been described in another study:
+
+  **In silico saturation mutagenesis of cancer genes**  
+  Ferran Muiños, Francisco Martinez-Jimenez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-Bigas  
+  URL: [https://www.nature.com/articles/s41586-021-03771-1](https://www.nature.com/articles/s41586-021-03771-1)
+
+## Content
+This repo contains the source code to reproduce the training and prediction steps of the boostDM-CH pipeline,
+starting from the output data coming after the pipeline of IntOGen-CH
+
+## Prerequisites
+
+#### HPC
+
+It is strongly recommended to run this pipeline in an HPC environment.
+
+#### Singularity
+
+The pipeline makes use of Singularity to handle software dependencies. 
+
+* Create a singularity image using the [Singularity](https://github.com/bbglab/boostdm-pipeline/blob/ch/containers_build/boostdm/Singularity) recipe:
+```
+$ cd containers_build/boostdm/
+$ sudo singularity build boostdm.sif Singularity
+```
+* Copy the singularity image in the root
+```
+$ cp containers_build/boostdm/boostdm.sif .
+``` 
+
+#### Nextflow
+
+The pipeline runs with the [nextflow](https://www.nextflow.io/) workflow orchestrator. 
+The boostDM-CH pipeline has been tested with nextflow version 20.07.1 which you can install e.g. with conda:
+```
+conda install -c bioconda nextflow=20.07.1
+```
+
+## Running the pipeline
+
+#### Configuration
+
+Consider the following adjustments before running the workflow:
+
+* Adjust the values in the **nextflow.config** file. In particular, check the following:
+
+   * env: **INTOGEN_DATASETS**, **DRIVERS_PATH** and **COHORTS_PATH** paths
+   * singularity: **cacheDir** and **runOptions** paths.
+   * process: make sure **container** matches the name of the singularity image file.
+   * profile: include any custom execution profiles in the **config/** folder
+
+* Adjust the **OUTPUT** parameter to match the **output/** folder in the **boostdm.nf** nextflow script.
+
+* Execution profiles are defined in the **config/** folder. Make sure that your custom profile matches 
+the computational resources available.
+
+#### Run with nextflow
+
+```
+$ nextflow run boostdm.nf -profile <execution-profile> -resume
+```
+
+#### Run details
+
+When the pipeline finishes, nextflow provides a summary of all the processes run in the file **trace.txt**.