Initial release of nf-core/seqsubmit

Added

The pipeline supports four submission modes via dedicated workflows:

• mags — Metagenome Assembled Genomes submission (GENOMESUBMIT)
• bins — Metagenomic bins submission (GENOMESUBMIT)
• metagenomic_assemblies — Assembly submission (ASSEMBLYSUBMIT)
• reads — Raw sequencing reads submission (READSUBMIT)

Key features:

• Automatic study registration with ENA when no existing study accession is provided
• Support for public and private data submissions, including configurable release dates
• Coverage calculation from reads when not provided directly (via coverm)
• Completeness/contamination estimation and taxonomy inference for MAGs/bins (via CheckM2 and CAT_pack) when metadata is incomplete
• Credentials handled securely via Nextflow secrets (ENA_WEBIN, ENA_WEBIN_PASSWORD)
• Full nf-core compatibility: runs with conda, Docker, and Singularity

Authors:

• Sofia Ochkalova
• Ekaterina Sakharova
• Tim Rozday
• Martin Beracochea

Reviewers:

• Evangelos Karatzas
• James Fellows Yates
• Matthias De Smet