Update and restructure docs for v1.0 release#83
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…istics and coverage calculation
…update metadata schema
KateSakharova
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Jul 9, 2026
KateSakharova
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Thank you, Sonya!!! I have changed a base to 1.0.0 because I already have some changes there. We will merge it to dev after all fixes.
- We do not have READSUBMIT in
methods.md. Do we have something to write about? - We probably need to structure parts in alphabetic order: Assembly, Genome, Read
or in submission order: Read, Assembly, Genome. I would say first one probably is quite universal ... and all docs should follow that order.
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| #### `mags` and `bins` modes (`GENOMESUBMIT`) | ||
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| - **Co-assemblies**: MAGs/bins generated from co-assemblies are not supported. The pipeline currently expects each MAG/bin to be derived from an assembly generated from a single run. |
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I would point to your PR and say it is in development
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| - **Co-assemblies**: MAGs/bins generated from co-assemblies are not supported. The pipeline currently expects each MAG/bin to be derived from an assembly generated from a single run. | ||
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| - **Eukaryotic and viral bins/MAGs**: Submitting eukaryotic or viral genomes that require additional metadata generation is not supported. For such genomes tRNA and rRNA prediction, quality assessment (completeness/contamination estimation) and taxonomy assignment are not implemented. If all the required metadata (`completeness`, `contamination`, `stats_generation_software`, `RNA_presence` and `NCBI_lineage`) is already provided in the samplesheet, eukaryotic and viral bins/MAGs can still be submitted normally. |
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Maybe we should link issues here? We kind of target to fix those
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| - **Reads in non-FASTQ formats**: Only reads provided as FASTQ (`.fastq.gz`) can be submitted. Other formats (e.g. BAM) are not supported as input. | ||
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| ## Credits |
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I think we have a quite big readme and need a table of contents in the beggining of file (it was also one of James's suggestions)
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Documentation improvements:
README.mddescribing resource-intensive steps, recommendations for HPC usage, and ENA submission rate limits.README.mdoutlining unsupported data types and scenarios for each pipeline mode, including details on co-assemblies, eukaryotic/viral bins, single-contig assemblies, and input format restrictions.methods.mddocument.methods.mdtousage.md.Resolves #81
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).