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Fix schema single-end logic
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@yolandabq te he añadido de revisora. Echale un vistazo sobretodo a la documentación. También te pediría si puedes ejecutar alguna prueba tu en tu máquina, pasándole los paths a parte. |
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Pull Request Overview
This PR adds support for CIBERER group-specific profiles to the pipeline, with an initial implementation of the tblab profile. The changes enable different CIBERER research groups to run the pipeline with their institution-specific annotation databases and configurations.
- Adds a new
tblabprofile configuration with comprehensive annotation database parameters - Provides template configuration files and documentation for setting up the tblab profile
- Fixes a logic error in the
single_enddetection for FASTQ files - Updates documentation links to use the correct repository name
Reviewed Changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| subworkflows/local/input_check.nf | Corrects the logic for determining single-end vs paired-end sequencing data |
| nextflow.config | Includes the new CIBERER groups configuration file |
| main.nf | Adds conditional initialization for tblab profile-specific variables |
| docs/tblab_parameters.md | Documents all parameters required for the tblab profile |
| docs/annotation.md | Updates repository URL in documentation link |
| conf/CIBERER_templates/tblab_parameters.config | Provides template configuration file for tblab users |
| conf/CIBERER_groups.config | Implements the tblab profile with annotation database paths and VEP settings |
| README.md | Adds reference to CIBERER group profiles documentation |
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| // Define extra variables if using CIBERER groups profiles | ||
| if (workflow.profile.contains('tblab')) { | ||
| def extra_files = params.extra_files() |
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The variable extra_files is assigned but never used within this conditional block or elsewhere in the visible code. This creates dead code that serves no purpose. Either remove this declaration if it's not needed, or if it's intended for future use, add a comment explaining its purpose.
| def extra_files = params.extra_files() | |
| // (removed unused assignment of extra_files) |
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Esta línea para qué es?
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creo que era para evaluar el contenido de params.extra_files(). Si no recuerdo mal, hasta que no se ejecutaba algo así, no se le asignaba el valor a las variables. Esto me permitía controlar el punto donde se definían los valores.
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| ## tblab Profile | ||
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| This profile runs the pipeline with the annotation databases and resources used by the Translational Bioinformatics Lab (tblab) at the Fundación Jiménez Díaz (FJD) (date 06/11/2025). We have included a [template](https://github.com/CIBERER/nf-CBRA-snvs/blob/conf/CIBERER_templates/tblab_parameters.config) with the required annotation files used to run this profile. |
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The GitHub URL is malformed - it's missing the branch name between 'blob' and the path. The URL should be something like https://github.com/CIBERER/nf-CBRA-snvs/blob/main/conf/CIBERER_templates/tblab_parameters.config with an actual branch name (e.g., 'main', 'master', 'dev') inserted after 'blob/'.
| This profile runs the pipeline with the annotation databases and resources used by the Translational Bioinformatics Lab (tblab) at the Fundación Jiménez Díaz (FJD) (date 06/11/2025). We have included a [template](https://github.com/CIBERER/nf-CBRA-snvs/blob/conf/CIBERER_templates/tblab_parameters.config) with the required annotation files used to run this profile. | |
| This profile runs the pipeline with the annotation databases and resources used by the Translational Bioinformatics Lab (tblab) at the Fundación Jiménez Díaz (FJD) (date 06/11/2025). We have included a [template](https://github.com/CIBERER/nf-CBRA-snvs/blob/main/conf/CIBERER_templates/tblab_parameters.config) with the required annotation files used to run this profile. |
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Esto solo funcionará cuando esté en el master. De todas formas, el path estaba mal y lo he actualizado como decía copilot.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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| // dbscSNV | ||
| dbscSNV = "" | ||
| dbscSNV_tbi = { -> "${params.dbscSNV}.tbi" } |
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Las flechitas (->) son para algo??
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Sí. Todo esto es para permitir pasar los paths en otro nextflow.config. En este caso, dbscSNV_tbi lo define, si no se le pasa aparte, como dbscSNV + .tbi
Updated the institution name from 'Fundación Jiménez Díaz' to 'Instituto de Investigación Sanitaria Fundación Jiménez Díaz'.
Correct path for future configuration
Is there an existing PR for this?
Types of changes:
Description
He definido el perfil de TBLAB. He tenido que hacer algunos cambios al config. También he añadido la documentación.
Checklist:
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