dānaSeq: containerized Nextflow pipelines for environmental metagenomics, metatranscriptomics and amplicon sequencing

Motivation: Environmental sequencing projects often combine nanopore and Illumina metagenomes, metatranscriptomes and marker-gene amplicons from the same samples. Each data type needs its own processing chain, and the chains must exchange products and run reproducibly on shared high-performance computing (HPC) systems. Results: dānaSeq is a suite of six Nextflow DSL2 pipelines: real-time nanopore read processing (nanopore_live), long-read co-assembly (nanopore_assembly), short-read assembly (illumina_assembly), technology-agnostic recovery and annotation of metagenome-assembled genomes (mag_analysis), metatranscriptome quantification against suite-produced references (illumina_rna) and amplicon denoising (illumina_amplicon). The pipelines exchange data through documented files: an assembly FASTA, a MetaBAT2-format depth table and BAM files feed mag_analysis, and assembly or MAG output directories serve as mapping references for illumina_rna. Each pipeline writes its results, a run manifest and Nextflow execution reports to one output directory, and a single script downloads the 22 reference databases. Each pipeline runs from a Bash launcher using conda environments or Docker/Apptainer images published to the GitHub Container Registry. On Slurm clusters, a launcher call runs inside one allocation with a node-local work directory, and finished results are cached so that resubmitted jobs reuse completed stages; three pipelines can also submit each task as its own Slurm job. Four pipelines export data for browser dashboards that can be served as static sites or published to microscape.app. Availability and implementation: dānaSeq is released under the MIT license at https://github.com/rec3141/danaSeq (this description corresponds to release v1.3.0, https://github.com/rec3141/danaSeq/releases/tag/v1.3.0); documentation at https://rec3141.github.io/danaSeq/.