Add EvolvDx methylation QC subworkflow and supporting modules

CHANGELOG.md

@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## EvolvDx fork (`evolvdx-main`)
+
+- Rebuilt on nf-core/methylseq 4.2.0. Added the EvolvDx QC steps (`--run_methylqc`, `--run_cpg_coverage`, `--run_methsnsv`, `--run_picardhs_report`), the `evolvdx*` profiles and the custom genomes. See `EVOLVDX.md`.
+- `--run_methylqc` results now appear in the MultiQC report under "EvolvDx methylation QC": General Stats columns (spike-in and mean CpG methylation, CpG depth, % CpGs in repeats), CpG read metrics, methylation and depth distributions, M-bias, methylation by chromosome, Twist annotation and tiled beta values (new `METHYLQC_MULTIQC` module).
+- methyl_qc fixes: "Methylated CpG Count" in `chr_percent_df.csv` no longer repeats the CpG count; read metrics are now computed from read counts (the old "% of total reads that are partial" was built from the bedGraph methylation column); tiles missing from a sample are left empty instead of set to beta 0; cohort inputs are ordered by sample id.
+- methyl_qc modules reformatted with named emits, `when:` blocks and clean `versions.yml`; `env/exo` Dockerfiles and the methylkit environment now build.
+
 ## [v4.2.0](https://github.com/nf-core/methylseq/releases/tag/4.2.0) - [2025-12-05]
 
 ### Bug fixes & refactoring

EVOLVDX.md

@@ -0,0 +1,46 @@
+# EvolvDx additions to nf-core/methylseq
+
+This fork tracks `nf-core/methylseq` (`upstream` remote). All EvolvDx changes live on the
+`evolvdx-main` branch; `master` mirrors nf-core. Keep upstream files untouched where possible
+so that new releases merge cleanly.
+
+## Running
+
+```bash
+nextflow run EVolvDx/methylseq -r evolvdx-main -profile evolvdx,docker --input samplesheet.csv --outdir results
+```
+
+| Profile | Purpose |
+|---|---|
+| `evolvdx` | Production defaults: `bwameth`, `grch38_core_bs_controls`, `clip_r1 20`, `clip_r2 15`, EvolvDx QC steps on |
+| `evolvdx_test` | Small NSQCAM529 subsample from S3, EvolvDx steps and Picard HS report on |
+| `evolvdx_aws`, `evolvdx_aws_500gb` | AWS Batch queues (`conf/evolvdx/`) |
+
+Plain nf-core behaviour is unchanged unless one of the flags below is set.
+
+## What was added
+
+| Flag | Component | Notes |
+|---|---|---|
+| `--run_methylqc` | `subworkflows/local/methylqc` | Cohort-level methylKit/HDF5 merge, control stats, read stats, tiled stats, Twist and repeat annotation, per-chromosome histograms, all summarised in the MultiQC report ("EvolvDx methylation QC") with the raw tables and plots in `methqc/`. The samplesheet's optional `group` column sets the methylKit treatment groups. Needs `--aligner bwameth`; runs a second MethylDackel extraction for the methylKit files (do not also pass `--methyl_kit`, which would suppress the bedGraph output). |
+| `--run_cpg_coverage` | `subworkflows/local/cpg_cov` | CpG island intersect and per-base coverage. Needs `--cpg_island_bed`. |
+| `--run_methsnsv` | `modules/local/exo/methsnsv.nf` | Methylation SNV/SV statistics from MethylDackel bedGraphs. |
+| `--run_picardhs_report` | `modules/local/exo/custom_multiqc` | EvolvDx Picard HS tables in MultiQC. Needs `--run_targeted_sequencing --collecthsmetrics`. |
+
+Also: `conf/evolvdx/custom_genomes.config` (S3 genomes under `--exogenomes_base`), `bin/` analysis
+scripts, `assets/multiqc/` headers, `env/` Dockerfiles, `analysis/notebooks/`, `scripts/`, and
+`tests/samplesheets`, `tests/scripts`.
+
+## Deliberately not carried over from the old fork
+
+- `PICARD_HS` subworkflow and local Picard modules: replaced by upstream `TARGETED_SEQUENCING`
+  (`--run_targeted_sequencing --target_regions_file ... --collecthsmetrics`). Upstream uses one
+  regions file for both bait and target; the old fork had separate `probe_bed` and `target_bed`.
+- `SUBREAD_FEATURECOUNTS` (gene counts on the methylation BAMs).
+- `cegx` and `epignome` library presets (use explicit `--clip_r1/--clip_r2/...`).
+- `with_hybcap`, `probe_bed`, `target_bed`, `fai` params, and the `max_cpus/max_memory/max_time` params.
+
+## Known upstream issues (present in nf-core/methylseq 4.2.0 itself)
+
+`nextflow lint` reports errors in `modules/nf-core/rastair/mbiasparser/main.nf`, the `aws_batch`
+profile include (`conf/aws/batch/nextflow.config` is missing) and `nf-test.config`.