Oncodrive3D 1.0.4__tar.gz → 1.0.5__tar.gz

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/Dockerfile

@@ -30,7 +30,7 @@ COPY --from=build-stage /oncodrive3d/dist /oncodrive3d/dist
 WORKDIR /oncodrive3d
 
 # Install oncodrive3d
-RUN pip install dist/*.tar.gz
+RUN pip install --no-cache-dir dist/*.tar.gz
 
 # Create required directories
 RUN install -d -m 0755 "$BGDATA_LOCAL" "$BBGLAB_HOME"

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/LICENSE

@@ -1,6 +1,8 @@
-Oncodrive3D is the property of the Institute for Research in Biomedicine (IRB Barcelona), which hold the copyright thereto.
 Copyright (C) 2024 Institute for Research in Biomedicine (IRB Barcelona)
 
+Oncodrive3D is the property of the Institute for Research in Biomedicine 
+(IRB Barcelona), which hold the copyright thereto.
+
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as
 published by the Free Software Foundation, either version 3 of the

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Oncodrive3D
-Version: 1.0.4
+Version: 1.0.5
 Summary: Oncodrive3D is a method designed to analyse patterns of somatic mutations across tumors to identify three-dimensional (3D) clusters of missense mutations and detect genes that are under positive selection.
 Project-URL: Homepage, https://github.com/bbglab/clustering_3d
 Project-URL: Repository, https://github.com/bbglab/clustering_3d
@@ -45,9 +45,6 @@ The method leverages **AlphaFold 2-predicted protein structures** and Predicted
 
 ---
 
-## License
-
-Oncodrive3D is available to the general public subject to certain conditions described in its [LICENSE](LICENSE).
 
 ## Requirements
 
@@ -99,7 +96,7 @@ Additionally, you may need to install additional development tools. Depending on
 This step build the datasets necessary for Oncodrive3D to run the 3D clustering analysis. It is required once after installation or whenever you need to generate datasets for a different organism or apply a specific threshold to define amino acid contacts.
 
 > [!WARNING]
-> This step is highly time- and resource-intensive, requiring a significant amount of free disk space. It will download a large amount of data, including AlphaFold-predicted structures and reference genomes (if not already cached). Ensure sufficient resources are available before proceeding, as insufficient capacity may result in extended runtimes or processing failures.
+> This step is highly time- and resource-intensive, requiring a significant amount of free disk space and computational power. It will download and process a large amount of data. Ensure sufficient resources are available before proceeding, as insufficient capacity may result in extended runtimes or processing failures.
 
 > [!NOTE]
 > The first time that you run Oncodrive3D building dataset step with a given reference genome, it will download it from our servers. By default the downloaded datasets go to`~/.bgdata`. If you want to move these datasets to another folder you have to define the system environment variable `BGDATA_LOCAL` with an export command.
@@ -240,51 +237,16 @@ Check the output in the `test/output/` directory to ensure the analysis complete
 
 ## Parallel Processing on Multiple Cohorts
 
-Oncodrive3D can be run in parallel on multiple cohorts using [Nextflow](https://www.nextflow.io/). This approach enables efficient, reproducible and scalable analysis across datasets.
-
-### Requirements
-
-1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) (version `23.04.3` was used for testing).
-2. Install and set up either or both:
-   - [Singularity](https://sylabs.io/guides/latest/user-guide/installation.html)  
-      Pull the Oncodrive3D Singularity image from Docker Hub:
-
-      ```
-      singularity pull oncodrive3d.sif docker://bbglab/oncodrive3d:latest
-      ```
+This repository provides a [Nextflow](https://www.nextflow.io/) pipeline to run Oncodrive3D in parallel across multiple cohorts, enabling efficient, reproducible and scalable analysis across datasets.  
 
-   - [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)  
-      Ensure Oncodrive3D is installed in your Conda environment and update the `params` section of the `nextflow.config` file to point to your Conda installation:
-
-         ```groovy
-         params {
-            ...
-            conda_env = '/path/to/conda/environment/with/oncodrive3d' 
-            ...
-         }
-         ```
-
-      Replace `/path/to/conda/environment/with/oncodrive3d` with the path to your Conda environment. Alternatively, you can provide it as a command-line argument.
-
-
-### Test Run
-
-Run a test to ensure that everything is set up correctly and functioning as expected:
-
-```
-cd oncodrive3d_pipeline
-nextflow run main.nf -profile test,container --data_dir <build_folder>
-```
-
-Replace `<build_folder>` with the path to the Oncodrive3D datasets built in the [building datasets](#building-datasets) step.
-If you prefer to use Conda, replace `container` in the `-profile` argument with `conda`.
+For more information, refer to the [Oncodrive3D Pipeline](https://github.com/bbglab/oncodrive3d/tree/master/oncodrive3d_pipeline/) documentation.
 
 ### Usage
 
 ---
 
 > [!WARNING]
-> When using the Nextflow script, ensure that your input files are organized in the following directory structure:
+> When using the Nextflow script, ensure that your input files are organized in the following directory structure (you only need either the `maf/` or `vep/` directory):
 > 
 > ```plaintext
 > input/
@@ -311,7 +273,7 @@ Example of run using VEP output as input and MANE Select transcripts:
   
 Options:
   --indir PATH                    Path to the input directory including the subdirectories 
-                                  `maf` or `vep` and `mut_profile`. 
+                                  `maf/` or `vep/` and `mut_profile/`. 
   --outdir PATH                   Path to the output directory. 
                                   Default: run_<timestamp>/
   --cohort_pattern STR            Pattern expression to filter specific files within the 
@@ -320,14 +282,27 @@ Options:
   --data_dir PATH                 Path to the Oncodrive3D datasets directory, which includes 
                                   the files compiled during the building datasets step.
                                   Default: ${baseDir}/datasets/
-  --container PATH                Path to the Singularity image with Oncodrive3D installation. 
-                                  Default: ${baseDir}/../oncodrive3d.sif
   --max_running INT               Maximum number of cohorts to process in parallel.
                                   Default: 5
   --cores INT                     Number of CPU cores used to process each cohort. 
                                   Default: 10
   --memory STR                    Amount of memory allocated for processing each cohort. 
                                   Default: 70GB
+  --vep_input BOOL                Use `vep/` subdir as input and select transcripts matching 
+                                  the Ensembl transcript IDs in Oncodrive3D built datasets. 
+                                  Default: false
+  --mane BOOL                     Prioritize structures corresponding to MANE transcrips if 
+                                  multiple structures are associated to the same gene.
+                                  Default: false
   --seed INT:                     Seed value for reproducibility.
                                   Default: 128
-```
+```
+
+
+## License
+
+Oncodrive3D is available to the general public subject to certain conditions described in its [LICENSE](LICENSE).
+
+
+## Citation 
+If you use Oncodrive3D in your research, please cite the original paper: [Oncodrive3D: Fast and accurate detection of structural clusters of somatic mutations under positive selection](https://www.biorxiv.org/content/10.1101/2025.01.11.632354v2).

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/README.md

@@ -10,9 +10,6 @@ The method leverages **AlphaFold 2-predicted protein structures** and Predicted
 
 ---
 
-## License
-
-Oncodrive3D is available to the general public subject to certain conditions described in its [LICENSE](LICENSE).
 
 ## Requirements
 
@@ -64,7 +61,7 @@ Additionally, you may need to install additional development tools. Depending on
 This step build the datasets necessary for Oncodrive3D to run the 3D clustering analysis. It is required once after installation or whenever you need to generate datasets for a different organism or apply a specific threshold to define amino acid contacts.
 
 > [!WARNING]
-> This step is highly time- and resource-intensive, requiring a significant amount of free disk space. It will download a large amount of data, including AlphaFold-predicted structures and reference genomes (if not already cached). Ensure sufficient resources are available before proceeding, as insufficient capacity may result in extended runtimes or processing failures.
+> This step is highly time- and resource-intensive, requiring a significant amount of free disk space and computational power. It will download and process a large amount of data. Ensure sufficient resources are available before proceeding, as insufficient capacity may result in extended runtimes or processing failures.
 
 > [!NOTE]
 > The first time that you run Oncodrive3D building dataset step with a given reference genome, it will download it from our servers. By default the downloaded datasets go to`~/.bgdata`. If you want to move these datasets to another folder you have to define the system environment variable `BGDATA_LOCAL` with an export command.
@@ -205,51 +202,16 @@ Check the output in the `test/output/` directory to ensure the analysis complete
 
 ## Parallel Processing on Multiple Cohorts
 
-Oncodrive3D can be run in parallel on multiple cohorts using [Nextflow](https://www.nextflow.io/). This approach enables efficient, reproducible and scalable analysis across datasets.
-
-### Requirements
-
-1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) (version `23.04.3` was used for testing).
-2. Install and set up either or both:
-   - [Singularity](https://sylabs.io/guides/latest/user-guide/installation.html)  
-      Pull the Oncodrive3D Singularity image from Docker Hub:
-
-      ```
-      singularity pull oncodrive3d.sif docker://bbglab/oncodrive3d:latest
-      ```
+This repository provides a [Nextflow](https://www.nextflow.io/) pipeline to run Oncodrive3D in parallel across multiple cohorts, enabling efficient, reproducible and scalable analysis across datasets.  
 
-   - [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)  
-      Ensure Oncodrive3D is installed in your Conda environment and update the `params` section of the `nextflow.config` file to point to your Conda installation:
-
-         ```groovy
-         params {
-            ...
-            conda_env = '/path/to/conda/environment/with/oncodrive3d' 
-            ...
-         }
-         ```
-
-      Replace `/path/to/conda/environment/with/oncodrive3d` with the path to your Conda environment. Alternatively, you can provide it as a command-line argument.
-
-
-### Test Run
-
-Run a test to ensure that everything is set up correctly and functioning as expected:
-
-```
-cd oncodrive3d_pipeline
-nextflow run main.nf -profile test,container --data_dir <build_folder>
-```
-
-Replace `<build_folder>` with the path to the Oncodrive3D datasets built in the [building datasets](#building-datasets) step.
-If you prefer to use Conda, replace `container` in the `-profile` argument with `conda`.
+For more information, refer to the [Oncodrive3D Pipeline](https://github.com/bbglab/oncodrive3d/tree/master/oncodrive3d_pipeline/) documentation.
 
 ### Usage
 
 ---
 
 > [!WARNING]
-> When using the Nextflow script, ensure that your input files are organized in the following directory structure:
+> When using the Nextflow script, ensure that your input files are organized in the following directory structure (you only need either the `maf/` or `vep/` directory):
 > 
 > ```plaintext
 > input/
@@ -276,7 +238,7 @@ Example of run using VEP output as input and MANE Select transcripts:
   
 Options:
   --indir PATH                    Path to the input directory including the subdirectories 
-                                  `maf` or `vep` and `mut_profile`. 
+                                  `maf/` or `vep/` and `mut_profile/`. 
   --outdir PATH                   Path to the output directory. 
                                   Default: run_<timestamp>/
   --cohort_pattern STR            Pattern expression to filter specific files within the 
@@ -285,14 +247,27 @@ Options:
   --data_dir PATH                 Path to the Oncodrive3D datasets directory, which includes 
                                   the files compiled during the building datasets step.
                                   Default: ${baseDir}/datasets/
-  --container PATH                Path to the Singularity image with Oncodrive3D installation. 
-                                  Default: ${baseDir}/../oncodrive3d.sif
   --max_running INT               Maximum number of cohorts to process in parallel.
                                   Default: 5
   --cores INT                     Number of CPU cores used to process each cohort. 
                                   Default: 10
   --memory STR                    Amount of memory allocated for processing each cohort. 
                                   Default: 70GB
+  --vep_input BOOL                Use `vep/` subdir as input and select transcripts matching 
+                                  the Ensembl transcript IDs in Oncodrive3D built datasets. 
+                                  Default: false
+  --mane BOOL                     Prioritize structures corresponding to MANE transcrips if 
+                                  multiple structures are associated to the same gene.
+                                  Default: false
   --seed INT:                     Seed value for reproducibility.
                                   Default: 128
-```
+```
+
+
+## License
+
+Oncodrive3D is available to the general public subject to certain conditions described in its [LICENSE](LICENSE).
+
+
+## Citation 
+If you use Oncodrive3D in your research, please cite the original paper: [Oncodrive3D: Fast and accurate detection of structural clusters of somatic mutations under positive selection](https://www.biorxiv.org/content/10.1101/2025.01.11.632354v2).

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/docs/run_input_output.md

@@ -27,10 +27,10 @@ vep --dir <vep_data> -i <input_vcf> --offline --cache -o <output>.vep.tsv \
 
 The output of VEP should be filtered so that each mutation is mapped to a single transcript. Additionally, it should be parsed to conform to the MAF format and include at least the following fields:
 
-- `Hugo_Symbol`: HUGO symbol for the gene.
-- `Variant_Classification`: Translational effect of variant allele.
-- `Transcript_ID`: Ensembl ID of the transcript affected by the variant.
-- `HGVSp_Short`: The protein sequence of the variant in HGVS recommended format using 1-letter amino-acid codes.
+- **Hugo_Symbol**: HUGO symbol for the gene.
+- **Variant_Classification**: Translational effect of variant allele.
+- **Transcript_ID**: Ensembl ID of the transcript affected by the variant.
+- **HGVSp_Short**: The protein sequence of the variant in HGVS recommended format using 1-letter amino-acid codes.
 
 ### VEP File
 
@@ -168,38 +168,38 @@ CSV file (`<cohort>.3d_clustering_genes.csv`) containing the results of the anal
 
 It includes the following fields:
 
-- `Gene`: HUGO symbol or identifier of the gene being analyzed.
-- `Uniprot_ID`: Identifier for the gene's protein product in the UniProt database.
-- `pval`:  The p-value indicating the statistical significance of the gene in the 3D clustering analysis (lowest p-value among the residues of the gene).
-- `qval`: Adjusted p-value (q-value) to control for false discovery rate (FDR) using the Benjamini-Hochberg method.
-- `C_gene`: Binary label indicating if the gene is detected to be significant (by default if `q-value < 0.01`).
-- `C_pos`: List of protein positions of the gene clusters.
-- `C_label`: List of labels indicating the clump to which each cluster is grouped.
-- `Pos_top_vol`: Position of the most significant cluster.
-- `Score_obs_sim_top_vol`: 3D clustering score of the gene (normalized 3D clustering score of the residue with the lowest p-value; if multiple residues have the same lowest p-value, the maximum normalized 3D clustering score among those residues is used).
-- `Mut_in_gene`: Number of missense mutations in the gene.
-- `Clust_mut`: Number of missense mutations in significant clusters.
-- `Clust_res`: Number of residues detected as significant clusters.
-- `Mut_in_top_vol`: Number of missense mutations in the most significant cluster (in the volume of the residue with the lowest p-value).
-- `Mut_in_top_cl_vol`: Number of missense mutations in the clusters of the most significant clump (in the volume of residues of the clump that includes the residue with the lowest p-value).
-- `PAE_top_vol`: Weighted average predicted aligned error (PAE) between the residues in the volume of the most significant cluster.
-- `pLDDT_top_vol`: Weighted average predicted local distance difference test (pLDDT) between the residues in the volume of the most significant cluster.
-- `pLDDT_top_cl_vol`: Weighted average pLDDT between the residues in the volume of the most significant clump.
-- `Ratio_not_in_structure`: Diagnostic field rapresenting the proportion of mutations in the input file that are mapped to positions not covered by the structure.
-- `Ratio_WT_mismatch`: Diagnostic field rapresenting the proportion of mutations in the input file where the wild-type (WT) amino acid does not match the corresponding residue in the structural model.
-- `Mut_zero_mut_prob`: Diagnostic field rapresenting the proportion of mutations in the input file that are assigned a mutation probability of zero. This field is relevant only when a mutability configuration file is provided as input (`-m`, `--mutability_config_path`).  
-- `Pos_zero_mut_prob`: Diagnostic field reporting the mutated protein position with assigned a mutation probability of zero. This field is relevant only when a mutability configuration file is provided as input (`-m`, `--mutability_config_path`).  
-- `Cancer`: Cancer type.
-- `Cohort`: Cohort name.
-- `F`: Fragment of the AlphaFold predicted structure (1 = no fragmentation, *n*M = merged from *n* fragments).
-- `Transcript_ID`: Ensembl transcript ID provided in the input file.
-- `O3D_transcript_ID`: Ensembl trasncript ID mapped to the given gene in the Oncodrive3D built datasets.
-- `Transcript_status`: Transcripts mapping status indicating whether the transcript IDs matches between the input data and the Oncodrive3D built datasets. Possible values are:
+- **Gene**: HUGO symbol or identifier of the gene being analyzed.
+- **Uniprot_ID**: Identifier for the gene's protein product in the UniProt database.
+- **pval**:  The p-value indicating the statistical significance of the gene in the 3D clustering analysis (lowest p-value among the residues of the gene).
+- **qval**: Adjusted p-value (q-value) to control for false discovery rate (FDR) using the Benjamini-Hochberg method.
+- **C_gene**: Binary label indicating if the gene is detected to be significant (by default if `q-value < 0.01`).
+- **C_pos**: List of protein positions of the gene clusters.
+- **C_label**: List of labels indicating the clump to which each cluster is grouped.
+- **Pos_top_vol**: Position of the most significant cluster.
+- **Score_obs_sim_top_vol**: 3D clustering score of the gene (normalized 3D clustering score of the residue with the lowest p-value; if multiple residues have the same lowest p-value, the maximum normalized 3D clustering score among those residues is used).
+- **Mut_in_gene**: Number of missense mutations in the gene.
+- **Clust_mut**: Number of missense mutations in significant clusters.
+- **Clust_res**: Number of residues detected as significant clusters.
+- **Mut_in_top_vol**: Number of missense mutations in the most significant cluster (in the volume of the residue with the lowest p-value).
+- **Mut_in_top_cl_vol**: Number of missense mutations in the clusters of the most significant clump (in the volume of residues of the clump that includes the residue with the lowest p-value).
+- **PAE_top_vol**: Weighted average predicted aligned error (PAE) between the residues in the volume of the most significant cluster.
+- **pLDDT_top_vol**: Weighted average predicted local distance difference test (pLDDT) between the residues in the volume of the most significant cluster.
+- **pLDDT_top_cl_vol**: Weighted average pLDDT between the residues in the volume of the most significant clump.
+- **Ratio_not_in_structure**: Diagnostic field rapresenting the proportion of mutations in the input file that are mapped to positions not covered by the structure.
+- **Ratio_WT_mismatch**: Diagnostic field rapresenting the proportion of mutations in the input file where the wild-type (WT) amino acid does not match the corresponding residue in the structural model.
+- **Mut_zero_mut_prob**: Diagnostic field rapresenting the proportion of mutations in the input file that are assigned a mutation probability of zero. This field is relevant only when a mutability configuration file is provided as input (`-m`, `--mutability_config_path`).  
+- **Pos_zero_mut_prob**: Diagnostic field reporting the mutated protein position with assigned a mutation probability of zero. This field is relevant only when a mutability configuration file is provided as input (`-m`, `--mutability_config_path`).  
+- **Cancer**: Cancer type.
+- **Cohort**: Cohort name.
+- **F**: Fragment of the AlphaFold predicted structure (1 = no fragmentation, *n*M = merged from *n* fragments).
+- **Transcript_ID**: Ensembl transcript ID provided in the input file.
+- **O3D_transcript_ID**: Ensembl trasncript ID mapped to the given gene in the Oncodrive3D built datasets.
+- **Transcript_status**: Transcripts mapping status indicating whether the transcript IDs matches between the input data and the Oncodrive3D built datasets. Possible values are:
     - `Input_missing`: Transcript ID is missing from the input file.
     - `O3D_missing`: Transcript ID is missing from the Oncodrive3D built datasets.
     - `Mismatch`: Transcript ID in the input file does not match the transcript ID in the Oncodrive3D built datasets.
     - `Match`: Transcript ID in the input file matches the transcript ID in the Oncodrive3D built datasets.
-- `Status`: Processing status for 3D clustering analysis. Possible values are:
+- **Status**: Processing status for 3D clustering analysis. Possible values are:
     - `Processed`: The gene has been successfully processed, with a 3D clustering score and a p-value assigned.
     - `No_mut`: The gene contains one or no mutations.
     - `No_density`: The maximum number of mutations in the spatial volume of any residue is one or less.
@@ -220,27 +220,27 @@ CSV file (`<cohort>.3d_clustering_pos.csv`) containing the results of the analys
 
 It includes the following fields:
 
-- `Gene`: HUGO symbol or identifier of the gene being analyzed.
-- `Uniprot_ID`: Identifier for the gene's protein product in the UniProt database.
-- `Pos`: Protein position.
-- `Mut_in_gene`: Number of missense mutations in the gene.
-- `Mut_in_res`: Number of missense mutations in the residue.
-- `Mut_in_vol`: Number of missense mutations in the volume of the residue.
-- `Score`: 3D clustering score for the residue.
-- `Score_obs_sim`: Normalized 3D clustering score for the residue.
-- `pval`: The p-value of the residue in the 3D clustering analysis.
-- `C`: Binary label indicating whether the cluster at that residue is significant (1) or not (0). A cluster is marked as significant either because it meets the significance criteria directly or because it has been rescued by contributing mutations to another significant cluster.
-- `C_ext`: Binary label indicating whether the cluster has been rescued by contributing mutations to another significant cluster (1) or if it was significant on its own (0).
-- `Clump`: Identifier for the clump to which the cluster at that residue has been assigned.
-- `Rank` Rank used to perform the calculation of the normalized 3D clustering score and p-values. 
-- `Mut_in_cl_vol`: Number of missense mutations in the clusters of the clump to which the cluster has been assigned.
-- `Res_in_cl`: Positions of the clusters of the clump to which the cluster has been assigned.
-- `PAE_vol`: Weighted average predicted aligned error (PAE) of the residues in the volume of the cluster.
-- `pLDDT_res`: Predicted local distance difference test (pLDDT) of the residue.
-- `pLDDT_vol`: Weighted average pLDDT between the residues in the volume.
-- `pLDDT_cl_vol`: pLDDT between the residues in the volume of the most significant cluster.
-- `Cancer`: Cancer type.
-- `Cohort`: Cohort name.
+- **Gene**: HUGO symbol or identifier of the gene being analyzed.
+- **Uniprot_ID**: Identifier for the gene's protein product in the UniProt database.
+- **Pos**: Protein position.
+- **Mut_in_gene**: Number of missense mutations in the gene.
+- **Mut_in_res**: Number of missense mutations in the residue.
+- **Mut_in_vol**: Number of missense mutations in the volume of the residue.
+- **Score**: 3D clustering score for the residue.
+- **Score_obs_sim**: Normalized 3D clustering score for the residue.
+- **pval**: The p-value of the residue in the 3D clustering analysis.
+- **C**: Binary label indicating whether the cluster at that residue is significant (1) or not (0). A cluster is marked as significant either because it meets the significance criteria directly or because it has been rescued by contributing mutations to another significant cluster.
+- **C_ext**: Binary label indicating whether the cluster has been rescued by contributing mutations to another significant cluster (1) or if it was significant on its own (0).
+- **Clump**: Identifier for the clump to which the cluster at that residue has been assigned.
+- **Rank**: Rank used to perform the calculation of the normalized 3D clustering score and p-values. 
+- **Mut_in_cl_vol**: Number of missense mutations in the clusters of the clump to which the cluster has been assigned.
+- **Res_in_cl**: Positions of the clusters of the clump to which the cluster has been assigned.
+- **PAE_vol**: Weighted average predicted aligned error (PAE) of the residues in the volume of the cluster.
+- **pLDDT_res**: Predicted local distance difference test (pLDDT) of the residue.
+- **pLDDT_vol**: Weighted average pLDDT between the residues in the volume.
+- **pLDDT_cl_vol**: pLDDT between the residues in the volume of the most significant cluster.
+- **Cancer**: Cancer type.
+- **Cohort**: Cohort name.
 
 
 ## Supplementary Output

oncodrive3d-1.0.5/oncodrive3d_pipeline/README.md

@@ -0,0 +1,90 @@
+# Oncodrive3D Nextflow Pipeline
+
+This pipeline enables running Oncodrive3D in parallel across multiple cohorts using [Nextflow](https://www.nextflow.io/).
+
+## Requirements
+
+1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) (version `23.04.3` was used for testing).
+2. Install and set up either or both:
+   - [Singularity](https://sylabs.io/guides/latest/user-guide/installation.html)  
+   - [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)  
+      Ensure Oncodrive3D is installed in your Conda environment and update the `params` section of the `nextflow.config` file to point to your Conda installation:
+
+         ```groovy
+         params {
+            ...
+            conda_env = '/path/to/conda/environment/with/oncodrive3d' 
+            ...
+         }
+         ```
+
+      Replace `/path/to/conda/environment/with/oncodrive3d` with the path to your Conda environment. Alternatively, you can provide it as a command-line argument.
+
+
+## Test Run
+
+Run a test to ensure that everything is set up correctly and functioning as expected:
+
+```
+nextflow run main.nf -profile test,container --data_dir <build_folder>
+```
+
+Replace `<build_folder>` with the path to the Oncodrive3D datasets built in the [building datasets](#building-datasets) step.
+If you prefer to use Conda, replace `container` in the `-profile` argument with `conda`.
+
+## Usage
+
+---
+
+> [!WARNING]
+> When using the Nextflow script, ensure that your input files are organized in the following directory structure (you only need either the `maf/` or `vep/` directory):
+> 
+> ```plaintext
+> input/
+>   ├── maf/
+>   │   └── <cohort>.in.maf
+>   ├── vep/
+>   │   └── <cohort>.vep.tsv.gz
+>   └── mut_profile/
+>       └── <cohort>.sig.json
+> ```
+> 
+> - `maf/`: Contains mutation files with the `.in.maf` extension.
+> - `vep/`: Contains VEP annotation files with the `.vep.tsv.gz` extension, which include annotated mutations with all possible transcripts.
+> - `mut_profile/`: Contains mutational profile files with the `.sig.json` extension.
+
+---
+
+```
+Usage: nextflow run main.nf [OPTIONS]
+
+Example of run using VEP output as input and MANE Select transcripts:
+  nextflow run main.nf -profile container --data_dir <build_folder> --indir <input> \
+                       --vep_input true --mane true
+  
+Options:
+  --indir PATH                    Path to the input directory including the subdirectories 
+                                  `maf` or `vep` and `mut_profile`. 
+  --outdir PATH                   Path to the output directory. 
+                                  Default: run_<timestamp>/
+  --cohort_pattern STR            Pattern expression to filter specific files within the 
+                                  input directory (e.g., 'TCGA*' select only TCGA cohorts). 
+                                  Default: *
+  --data_dir PATH                 Path to the Oncodrive3D datasets directory, which includes 
+                                  the files compiled during the building datasets step.
+                                  Default: ${baseDir}/datasets/
+  --max_running INT               Maximum number of cohorts to process in parallel.
+                                  Default: 5
+  --cores INT                     Number of CPU cores used to process each cohort. 
+                                  Default: 10
+  --memory STR                    Amount of memory allocated for processing each cohort. 
+                                  Default: 70GB
+  --vep_input BOLEAN              Use `vep/` subdir as input and select transcripts matching 
+                                  the Ensembl transcript IDs in Oncodrive3D built datasets. 
+                                  Default: false
+  --mane                          Prioritize structures corresponding to MANE transcrips if 
+                                  multiple structures are associated to the same gene.
+                                  Default: false
+  --seed INT                      Seed value for reproducibility.
+                                  Default: 128
+```

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/oncodrive3d_pipeline/modules/o3d_chimerax_plot.nf

@@ -2,14 +2,9 @@ process O3D_CHIMERAX_PLOT {
     tag "ChimeraX plot $cohort"
     label 'process_low'
     queue 'bigmem,normal'
-    container params.container_chimerax  
     maxForks params.max_running
     publishDir "${params.outdir}/${params.outsubdir}", mode:'copy'
-
-    // conda "bioconda::oncodrive3d"                                                                                 // TODO: Update and test
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?      // TODO: Update and test
-    //     'https://depot.galaxyproject.org/singularity/oncodrive3d--py39hbf8eff0_0' :
-    //     'quay.io/biocontainers/oncodrive3d--py39hbf8eff0_0' }"
+    container 'docker.io/spellegrini87/oncodrive3d_chimerax:latest'
 
     input:
     tuple val(cohort), path(inputs), path(genes_csv), path(pos_csv), path(mutations_csv), path(miss_prob_json), path(seq_df_tsv)

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/oncodrive3d_pipeline/modules/o3d_plot.nf

@@ -2,14 +2,9 @@ process O3D_PLOT {
     tag "Plot $cohort"
     label 'process_low'
     queue 'bigmem,normal'
-    container params.container
     maxForks params.max_running
     publishDir "${params.outdir}/${params.outsubdir}", mode:'copy'
-
-    // conda "bioconda::oncodrive3d"                                                                                  // TODO: Update and test
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?       // TODO: Update and test
-    //     'https://depot.galaxyproject.org/singularity/oncodrive3d--py39hbf8eff0_0' :
-    //     'quay.io/biocontainers/oncodrive3d--py39hbf8eff0_0' }"
+    container 'docker.io/bbglab/oncodrive3d:latest'
 
     input:
     tuple val(cohort), path(inputs), path(genes_csv), path(pos_csv), path(mutations_csv), path(miss_prob_json), path(seq_df_tsv)
@@ -17,11 +12,12 @@ process O3D_PLOT {
     output:
     tuple val(cohort), path("**.summary_plot.png"), optional: true, emit: summary_plot
     tuple val(cohort), path("**.genes_plots/**.png"), optional: true, emit: genes_plot
-    // tuple val(cohort), path("**.associations_plots/**.logodds_plot.png"), optional: true, emit: logodds_plot
-    // tuple val(cohort), path("**.associations_plots/**.volcano_plot.png"), optional: true, emit: volcano_plot
-    // tuple val(cohort), path("**.associations_plots/**.volcano_plot_gene.png"), optional: true, emit: volcano_plot_gene
+    tuple val(cohort), path("**.associations_plots/**.logodds_plot.png"), optional: true, emit: logodds_plot
+    tuple val(cohort), path("**.associations_plots/**.volcano_plot.png"), optional: true, emit: volcano_plot
+    tuple val(cohort), path("**.associations_plots/**.volcano_plot_gene.png"), optional: true, emit: volcano_plot_gene
     tuple val(cohort), path("**.3d_clustering_pos.annotated.csv"), optional: true, emit: pos_annotated_csv
-    tuple val(cohort), path("**.uniprot_feat.tsv"), optional: true, emit: uniprot_feat_csv
+    tuple val(cohort), path("**.uniprot_feat.tsv"), optional: true, emit: uniprot_feat_tsv
+    tuple val(cohort), path("**.logreg_result.tsv"), optional: true, emit: logreg_tsv
     path "**.log", emit: log
 
     script:
@@ -38,7 +34,6 @@ process O3D_PLOT {
         -a ${params.annotations_dir} \\
         -o $prefix \\
         -c $cohort \\
-        --title $cohort \\
         --output_csv \\
         ${params.verbose ? '-v' : ''} \\
         $args

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/oncodrive3d_pipeline/modules/o3d_run.nf

@@ -1,16 +1,11 @@
 process O3D_RUN {
     tag "O3D $cohort"
     queue 'bigmem,normal'
-    container params.container
     cpus params.cores
     memory params.memory
     maxForks params.max_running
     publishDir "${params.outdir}/${params.outsubdir}", mode:'copy'
-
-    // conda "bioconda::oncodrive3d"                                                                                    // TODO: Update and test
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?         // TODO: Update and test
-    //     'https://depot.galaxyproject.org/singularity/oncodrive3d--py39hbf8eff0_0' :
-    //     'quay.io/biocontainers/oncodrive3d--py39hbf8eff0_0' }"
+    container 'docker.io/bbglab/oncodrive3d:latest'
 
     input:
     tuple val(cohort), path(inputs)

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/oncodrive3d_pipeline/nextflow.config

@@ -9,8 +9,6 @@ params {
     cohort_pattern        = "*"
     data_dir              = "${baseDir}/../datasets"                                                // CHANGE TO YOUR PATH
     annotations_dir       = "${baseDir}/../annotations"                                             // CHANGE TO YOUR PATH
-    container             = "${baseDir}/../oncodrive3d.sif"                                         // CHANGE TO YOUR PATH
-    container_chimerax    = "${baseDir}/../oncodrive3d_chimerax.sif"                                // CHANGE TO YOUR PATH
     conda_env             = '/path/to/conda/environment/with/oncodrive3d'                           // CHANGE TO YOUR PATH
     cores                 = 10
     memory                = "70G"

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/oncodrive3d_pipeline/validation.nf

@@ -18,38 +18,6 @@ def validatePaths(params) {
         }
     }
 
-    // Validate Oncodrive3D Singularity image
-    if (workflow.containerEngine == 'singularity') {
-        def imagePath = file(params.container)
-        if (!imagePath.exists()) {
-            error """
-            \u001B[31mERROR: The specified Oncodrive3D Singularity image does not exist:
-            ${params.container}
-
-            Please provide the path to the Oncodrive3D Singularity image. 
-            You can update 'params.container' in the 'nextflow.config' file or provide it as a command-line argument: 
-
-            nextflow run main.nf --container <singularity_image>\u001B[0m
-            """
-        }
-    }
-
-    // Validate Oncodrive3D with ChimeraX Singularity image
-    if (params.chimerax_plot == true) {
-        def image_chimeraxPath = file(params.container_chimerax)
-        if (!image_chimeraxPath.exists() || !image_chimeraxPath.isDirectory()) {
-            error """
-            \u001B[31mERROR: The specified ChimeraX Singularity image does not exist:
-            ${params.container_chimerax}
-
-            Please provide the path to the ChimeraX Singularity image. 
-            You can update 'params.container_chimerax' in the 'nextflow.config' file or provide it as a command-line argument: 
-
-            nextflow run main.nf --container_chimerax <singularity_image>\u001B[0m
-            """
-        }
-    }
-
     // Validate Oncodrive3D datasets path
     def dataPath = file(params.data_dir)
     if (!dataPath.exists() || !dataPath.isDirectory()) {

{oncodrive3d-1.0.4 → oncodrive3d-1.0.5}/oncodrive3d_pipeline/workflows/oncodrive3d.nf

@@ -29,8 +29,6 @@ workflow ONCODRIVE3D {
     ChimeraX plots     : ${params.chimerax_plot}
     Seed               : ${params.seed}
     Verbose            : ${params.verbose}
-    Container          : ${params.container}
-    Container ChimeraX : ${params.container_chimerax}
     Profile            : ${workflow.profile}
     """
     .stripIndent()
@@ -66,10 +64,11 @@ workflow ONCODRIVE3D {
         plot_summary = params.plot ? O3D_PLOT.out.summary_plot : Channel.empty()
         plot_genes = params.plot ? O3D_PLOT.out.genes_plot : Channel.empty()
         plot_pos_annotated = params.plot ? O3D_PLOT.out.pos_annotated_csv : Channel.empty()
-        plot_uniprot_feat = params.plot ? O3D_PLOT.out.uniprot_feat_csv : Channel.empty()
-        // logodds_plot = params.plot ? O3D_PLOT.out.logodds_plot : Channel.empty()
-        // volcano_plot = params.plot ? O3D_PLOT.out.volcano_plot : Channel.empty()
-        // volcano_plot_gene = params.plot ? O3D_PLOT.out.volcano_plot_gene : Channel.empty()
+        plot_uniprot_feat = params.plot ? O3D_PLOT.out.uniprot_feat_tsv : Channel.empty()
+        plot_logreg_tsv = params.plot ? O3D_PLOT.out.logreg_tsv : Channel.empty()
+        logodds_plot = params.plot ? O3D_PLOT.out.logodds_plot : Channel.empty()
+        volcano_plot = params.plot ? O3D_PLOT.out.volcano_plot : Channel.empty()
+        volcano_plot_gene = params.plot ? O3D_PLOT.out.volcano_plot_gene : Channel.empty()
         plot_logs = params.plot ? O3D_PLOT.out.log : Channel.empty()
 
         plot_chimerax_defattr = params.chimerax_plot ? O3D_CHIMERAX_PLOT.out.chimerax_defattr : Channel.empty()