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Docs, contributors and citations ahead of release review - #73
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@BenjaminWehnert1008 please approve review, this is all documentation-related only. Thanks a lot |
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I just implemented an updated seqdepth downsampling in the latest PR, to have smaller step sizes. We can update this screenshot one more time after merge.
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happy to update the screenshot already here, prior to merging
BenjaminWehnert1008
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Oct 7, 2026
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Docs, contributors and citations ahead of the release review
Preparation for the first release (#54): documentation, metadata and citations brought up to date with the current pipeline behaviour. No changes to pipeline code or results.
Changes
nextflow_schema.json,.nf-core.yml, the email template andro-crate-metadata.jsondocs/usage.md: samplesheet columns, reference and reading frame, mutagenesis types, and a detailed description of every step matching the current code; parameter details for fitness estimation (--min_counts,--output_pseudocount, see Parameter and samplesheet conventions #69)docs/output.md: rewritten from the test-profile output layout, includingdeepmutscan_report.html, error-correction outputs, mutscan and the variant effect inspection tool; new example figuresnextflow_schema.json: updated parameter descriptions (text only)CHANGELOG.md: v1.0.0 entries and dependency versionsCITATIONS.md: added BWA-MEM, VSEARCH, DiMSum, mutscan, edgeR, limma, R packages and others; consistent formattingdocs/pipeline_steps.md(merged intousage.md) and a straylog.txtRelated to #54, #69.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>). (CI)docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).