First pipeline release

[BenjaminWehnert1008]

First release: nf-core/deepmutscan v1.0.0

This PR merges dev into master for the first release of nf-core/deepmutscan. @MaximilianStammnitz and I would be very grateful for your release reviews 🙏🙂.

What this pipeline does

nf-core/deepmutscan processes deep mutational scanning (DMS) data from short-read sequencing of site-saturation mutagenesis libraries. It was primarily designed for shotgun sequencing of long open reading frames, where the variant library is randomly fragmented before sequencing (no tiling or barcoding), and it handles amplicon data in the same way. Importantly, because variant frequencies in shotgun sequencing data are often sparse – below 1 in 10,000 reads – and thus in the range of per-base sequencing error rates (Q30-Q40), we conceptualise and implement key single-nucleotide count error correction modules.

1. Pre-processing and counting: FastQC → BWA-MEM alignment to a gene-sized (small) reference → samtools filtering (MAPQ ≥ 30, no indels) → vsearch read-pair merging and re-alignment → variant counting with a light-weight pysam/polars counter (replaces GATK AnalyzeSaturationMutagenesis, column-compatible output) → annotation and filtering against the programmed codon library (--mutagenesis_type).
2. Error correction and library QC: single-nucleotide variant sequencing-error correction from read-linked "false double" mutants (maximum likelihood or empirical Bayes estimation) or from additionally supplied wildtype template sequencing data, with an interactive report; per-library QC plots (count heatmaps, positional coverage and count profiles, sequencing-depth rarefaction).
3. Fitness: default log-ratio estimator relative to a high-quality and high-count synonymous wildtype proxy, rescaled to synonymous = 0 / stop = −1; optional DiMSum (--dimsum) and mutscan edgeR/limma (--mutscan); optional interactive 3D variant effect inspection tool from a user-supplied structure (--pdb).
4. Reporting: A single, self-contained deepmutscan_report.html per run.

Testing

• -profile test: 50,000 read-pair subsamples of a minimal GID1A nicking-mutagenesis GluePCA experiment (2 input + 2 output libraries) on the deepmutscan branch of nf-core/test-datasets, with fitness, DiMSum, mutscan and the structure viewer switched on. nf-test snapshot test in tests/default.nf.test.
• -profile test_full: the complete GID1A experiment (3 input + 3 output libraries, ~480M read pairs) from ENA project PRJEB110196, linked from a samplesheet on the same test-datasets branch, with fitness, DiMSum, mutscan and the structure viewer switched on (Full-size test profile (test_full) and AWS full test #68).
• Test data PR: Add a full test samplesheet test-datasets#1972 (adds the test_full samplesheet and the GID1A AlphaFold DB structure used by --pdb).

Known follow-ups

The following issues are already on our list and we will address these over the coming weeks, so that the review can focus on the release itself:

• Template update to nf-core/tools 4.1.0 and re-linting #66
• Full-size test profile (test_full) and AWS full test #68
• Parameter and samplesheet conventions #69
• Planned extensions after v1.0.0: Overall efficiency tuning of the pipeline #70, Support for FACS / sort-seq data #67, SNV error mutational signature support #72, Enrich2 and rosace support #71.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests! (pipeline-level nf-test with the test profile)
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/deepmutscan branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint). (passes with nf-core/tools 4.0.2, the template version of this pipeline; see Template update to nf-core/tools 4.1.0 and re-linting #66 for 4.1.0)
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).

Many thanks in advance to the reviewers, and to @mirpedrol and @mashehu for their guidance along the way.