metagenomicspipeline - Metagenomics pipeline v1.0.0

Major update to the workflow: now works with single-end and paired-end reads, integrated Kraken2 and updated MetaPhlAn and HUMAnN versions. The nf-core modules for FastQC and MultiQC were updated.

Added

• Single-end reads input: Pipeline now automatically detects and processes both single-end and paired-end FASTQ files
• Kraken2: Taxonomic classification with different database options
• Bracken: Species-level abundance estimation from Kraken2 output
• Skip parameters: Added --skip_kraken2, --skip_metaphlan, --skip_humann options for flexible workflow execution
• Added process to merge all read counts in one table (after removal of host reads)
• Added -profile test and -profile test_full with test setup for HUMAnN database download, so that the size of the test db is a lot smaller.
• Ensured that -profile conda works, although container use (Apptainer/Singularity or Docker) is still recommended
• Conditional tool citations: Citations in MultiQC reports now reflect only the tools actually used in the run

Dependencies

• Fastp: Updated to version 1.0.1
• Seqkit: Updated to version 2.9.0
• MetaPhlAn: Updated to version 4.2.2
• HUMAnN: Updated to version 4.0.0-alpha (no biocontainer available, pulls from Dockerhub)
• Kraken2: Added version 2.1.6 (no biocontainer available, pulls from Dockerhub)
• Bracken: Added version 3.1
• Fastqc: Updated to version 0.12.1
• Multiqc: Updated to version 1.30

Deprecated

• The pipeline no longer merges gene family output of HUMAnN. With too many samples, this would result in out-of-memory crashes.
• StrainPhlAn was removed from this pipeline, I made a separate workflow for StrainPhlAn.

Full Changelog: https://github.com/barbarahelena/metagenomicspipeline/compare/v.0.5.0-beta...v.1.0.0

- Nextflow
Published by barbarahelena 7 months ago

metagenomicspipeline - First release

First release of this metagenomics pipeline. StrainPhlAn still under development, so by default skipped when running the pipeline.

- Nextflow
Published by barbarahelena about 2 years ago