ReleaseNotes

v2.3.0 - 2025-11-03

Changed the name from PRMeth_RF to the actual name RefFreeCellMix and added the corresponding citation.
Added 2 new modules, being Houseman’s CP equality and inequality. Before, to run these modalities you had to specify the –mod EpiDISH parameter. Now this parameter is deprecated and to run the above two tools you just have to specify the corresponding new flag –houseman_eq and –houseman_ineq.
Changed the Docker container of CIBERSORT module with the EpiDISH container since EpiDISH package contains the CIBERSORT modality.
Readapted the output directories and files in the modules/conf to have a more clear structure.
Added tests on each individual module in the tests/modules/ folder.
Added pipeline end-to-end tests and nf-test actions on PR and new release.

v2.2.0 - 2025-07-02

Added the test profile to test the pipeline on public, test data.
Removed unnecessary files from assets/ directory and updated the documentation.

v2.1.0 - 2025-06-18

🐛 Bug Fixes

Limma module: Modified container and module to prevent errors when --top exceeds the available number of DMRs.
FINDMARKERS module: Added the --sort_by delta_means flag. Previously, when using --only_hyper, markers were incorrectly sorted by chromosome location instead of delta means as intended. _Note: a GitHub issue should be opened in the wgbs_tools repository regarding this behavior.
convert_atlas container: Updated to properly handle the new entity structure (with _) introduced in version 2.0.0.
wgbstools subworkflow: Adjusted to include _ in the entity structure to avoid processing errors.
UXM subworkflow: Added params.ref_matrix to the conditional (if) gate, ensuring that the workflow proceeds when no DMR selection method is specified but a reference matrix is provided.
Preprocessing modules: Added sort -T /tmp/ to prevent sort from using unavailable directories. See related discussion.
CelFiE preprocessing: Included missing params.big_covs parameter.

🚀 Minor Improvements

MERGE_SAMPLES module: Renamed the step parameter for clarity and consistency with the latest container version.
Container cleanup: Removed unnecessary containers and added a /bin directory for utility scripts.
test_DMR.R script optimization: Reduced container size by removing tidyverse from test_DMR.R, keeping only tibble and dplyr.
Limma DMR selection: Introduced params.include_na parameter to allow merging of reference samples even when values are missing. This prevents excessive region filtering when the number of samples or entities is high.
FINDMARKERS module: Moved top parameter outside the main script, now passed to the function only when explicitly defined (not null or false).
COMBINE_FILES module: Changed the way output files are combined: now files are linked directly using Nextflow, eliminating the need for volume bindings.
Reference coverage option: Added support to use reference coverage files (--input) instead of rerunning the bismark_methylationextraction module. Applies when using wgbstools for DMR selection and meth_atlas (or other tools except UXM) for deconvolution.
Bulk sample filtering parameters: Replaced refree_min_counts and refree_min_cpgs with bulk_min_counts and bulk_min_cpgs for more flexible CpG and region filtering on bulk samples. By default they are both set to 0 (meaning, no filtering on the bulk samples).

🔄 Updates to MetDecode & CelFiE Subworkflows

Previously, only atlas markers present in all bulk samples were used for deconvolution.
Now, if a marker is missing in any bulk sample, a value of 0 is assigned (instead of NA) for both methylation and depth, ensuring smoother downstream processing.

v2.0.0 - 2024-12-26

Bugs fixed

Thanks to @kaschoof, major bug has been fixed in the TEST_PROCESSING module that was grouping according to wrong columns when more than 2 cell types are specified in the atlas.
Fixed problems with check_max function and base.config file not properly imported in nextflow.config
Updated bedtools container version to the version 2.29.2 to fix a bug present in the previous version (see #643).
Updated CelFiE container adding random seeds to make it generating reproducible results.
Updated the PRMeth container to solve a bug on the number of cells (ncells) parameters when using the NMF modality.
Updated nf-core schema plugin to version 2.2.0
Changed the function to read the input file (from meta.clone() to def meta)

New features

Added lib directory with two functions for parameters checking, string citations, string version, for dumping parameters .json file and for nfcore logo.
Added DSS as an alternative DMR selection tool.
Added UXM deconvolution tool, wgbs_tools as DMR selection tool and other modules to convert the structure from uxm-like to standard ref-based structure
Added MetDecode tool
Added possibility to start from a reference matrix already built.
Added possibility to start from a merged matrix with reference samples on columns and regions on rows.
In the entity column of the reference samples is now possible to include numbers.

Minor changes

Restructuring of the pipeline structure
Removed merging_approach and chunk_size flags from the documentation (not used anymore).
Changed parameter custom of the flag DMRselection into limma.
Added possibility of specifying “-sorted” and “-g” to the bedtools intersect in the preprocessing to keep the memory usage low when using big coverage files (e.g. WGBS covs).
Sort the columns of the matrices in MERGE_SAMPLES module to make the files always the same
Updated MERGE_SAMPLES container to always output sorted samples for reproducibility
Added gitignore, pre-commit and CODEOWNERS for PR
Added metromap to the README
Added instituional config options
Changed methyl_atlas into meth_atlas
Added prefix chr check between region file and coverage files in limma preprocessing

v1.0.1 - 2024-07-26

Parameters changes

nsamples parameter has been removed (it’s now automatically computed)

Speed of the preprocessing

The preprocessing of the reference and testing samples, including the preprocessing adopted in the reference-free tools, has been modified. It now uses bedtools and runs in bash. The preprocessing is now much faster (10x) and less computationally intensive (20x).
merge_samples container and module has been added to merge all the files together once they have been preprocessed in order to give to the deconv tools the entire reference and testing matrix.

Input files validation

The validation of the input and test_set files has been moved in the DNAmDeconv workflow. Moreover, the samples are now being passed one by one to the preprocessing step: this allows parallelization of these steps, reduces the amount of memory needed and ultimately avoid run out of memory issues.

limma DMRs

Version two of the container has been released. With this version, it’s now possible to perform DMR selection with even only one sample per group.

v1.0.0 - 2024-07-16

The DNAmDeconv pipeline is designed to perform DNA methylation deconvolution on bulk DNA samples. This pipeline uses a Nextflow framework to streamline and automate the analysis process, ensuring reproducible and efficient results.