Notice bibliographique
Résumé
This release modernizes nf-ionampliseq to DSL-2 standards with enhanced BLAST analysis capabilities, improved containerization, and better resource management. Key additions include BLAST database integration, enhanced variant calling options, and comprehensive process version tracking. Added [feat] BLASTN process to run blastn with consensus sequences against user-specifed DB (--blast_db). [feat] BLASTN_COVERAGE process and blast_coverage.py for summarizing BLAST results and generating MultiQC tables. [feat] fill-tags plugin for BCFTOOLS_FILTER and better filtering of variants for consensus sequence construction. [feat] SEQTK_SUBSEQ process for extracting reference sequences based on Mash screen results. [feat] CONSENSUS_MULTIQC process for enhanced consensus sequence reporting in MultiQC. [feat] Enhanced container support for Docker, Singularity, Apptainer, and Podman. [feat] Version tracking for all processes with versions.yml files. [config] comprehensive DSL2 module configuration in conf/modules.config. [config] new configuration parameters: blast_db, trim_primers, output_unmapped_reads. [config] variant calling options: minor_allele_fraction, major_allele_fraction, low_coverage. [config] enhanced container profiles for multiple container engines. [config] proper resource management with check_max function for memory, CPU, and time limits. [config] timestamped execution reports and timeline files in nextflow.config. Changes [docs] Comprehensive documentation overhaul with detailed parameter descriptions and external tool references [cleanup] Removed legacy plotting module and environment.yml file for simplified architecture. Use wgscovplot instead for better and interactive plotting of coverage stats and variants. [cleanup] Simplified TMAP process configuration using dynamic arguments parameter. [update] Repository and container registry references updated to CFIA-NCFAD organization [feat] Complete workflow modernization to DSL2 standards with proper process separation. [feat] Added new Docker build workflow in .github/workflows/docker.yml for improved container publishing and CI separation. [feat] Added support for building and using custom Docker images with updated samtools and TMAP/TVC binaries. [feat] Enhanced process version tracking: all major processes now emit versions.yml with tool versions for reproducibility. [feat] Improved error handling and retry strategies for all processes. [update] MultiQC process updated to support new BLAST coverage MultiQC table. [update] Bump version of workflow and dependencies for 2.0.0 release. [update] Repository renamed from peterk87/nf-ionampliseq to CFIA-NCFAD/nf-ionampliseq. [update] Nextflow version requirement updated to !>=22.10.1. [update] All processes now use proper container definitions with conda and container specifications. [update] Process resource labeling standardized (process_low, process_medium, process_high). [update] Input/output patterns standardized across all processes with proper emit declarations. [update] TMAP and TVC processes enhanced with better parameter handling and version tracking. [update] TMAP and TVC processes now use new Docker image ghcr.io/cfia-ncfad/nf-ionampliseq:2.0.0 with updated samtools and runtime dependencies. [update] MASH screen workflow restructured with separate sketching and screening processes. [update] FastQC process enhanced with memory optimization and version tracking. [update] Samtools processes standardized with consistent version tracking and output handling. [update] Mosdepth process optimized with improved output handling and version tracking. [update] Edlib processes enhanced with container support and version tracking. [update] Sample sheet processing improved with better error handling and validation. [docs] Documentation and help text for BLAST coverage analysis improved. [docs] Updated documentation to reflect new container build and usage instructions. [ci] Updated GitHub Actions CI tests. [ci] Moved Docker container build to separate workflow for improved CI/CD. [ci] CI now tests with multiple Nextflow versions 22.10.1 and latest stable (25.04.6 currently). Fixed [fix] Container compatibility issues across different container engines. [fix] Process resource allocation and memory management. [fix] Version tracking consistency across all processes. [fix] Input/output file handling and validation. [fix] MultiQC report generation and custom content integration. Dependencies [deps] Updated to Nextflow !>=22.10.1. [deps] Enhanced container support with multiple engine options. [deps] Standardized conda environment specifications across all processes. [deps] Added better version tracking for all bioinformatics tools. What's Changed DSL2 modernization, BLAST analysis, and enhanced containerization by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/1 Release 2.0.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/2 New Contributors @peterk87 made their first contribution in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/1 Full Changelog: https://github.com/CFIA-NCFAD/nf-ionampliseq/compare/1.0.1...2.0.0
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,005 | 0,013 |
| Méta-épidémiologie (sens strict) | 0,003 | 0,004 |
| Méta-épidémiologie (sens large) | 0,003 | 0,003 |
| Bibliométrie | 0,004 | 0,002 |
| Études des sciences et des technologies | 0,002 | 0,001 |
| Communication savante | 0,006 | 0,005 |
| Science ouverte | 0,006 | 0,004 |
| Intégrité de la recherche | 0,003 | 0,005 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,168 | 0,249 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».