ReleaseNotes

v2.6.2 - 2025-07-15

In-house modifications applied to nf-core/methylseq pipeline version v2.6.0

• Added parameter to deactivate PicardMarkduplicates module
• Added parameter to specify which sequencer has been used for PicardMarkduplicates module.
• Reordered the main Bismark Workflow.
• Added the optional Sequencing Saturation plots.
• Picard Markduplicates module has been added to Bismark subworflow(look at the module for more information).
• Bismark filter_non_conversion function has been added to the Bismark subworkflow. It can be activated specifing the flga --filter_non_conversion together with the minimum_count and percentage_cutoff parameters (see nextflow.conf and filter_non_conversion module for more information). When activated, it creates an output folder where it saves 3 files. The fitlered bam file is then used for the subsequent modules. It needs to be updated with a new version of Bismark (and the corresponding biocontainer) when it is released (there is a bug in the current version, see the issue #688) since now it’s not using an official Bismark biocontainer.

v2.6.0 - 2024-01-05

Bug fixes & refactoring

• 🛠 Copy methylKit-compatible files to publishDir #357
• 🐛 fix ignore_r1 and ignore_3prime_r1 variable expansion #359

v2.5.0 - 2023-10-18

Pipeline Updates

• 🔄 Updated template to nf-core/tools v2.9
• 🔄 Updated template to nf-core/tools v2.10
• 🔧 Updated nf-core modules for FastQC, samtools sort, samtools flagstat
  • ❌ Removes problematic -m memory assignment for samtools sort #81
• 🧾 Use fromSamplesheet from nf-validation #341
• 🚀 Update Maintainers and add CODEOWNERS #345
• ⚙️ Update schema to utilize exists and add more patterns #342
• 📁 Support pipeline-specific configs #343

Bug fixes & refactoring

• 🛠️ Added publishing of coverage (*cov.gz) files for NOMe-seq filtered reads for coverage2cytosine
• 🛠️ Wrong display values for “zymo” and “em_seq” presets on help page #335
• 📚 Use new Citation tools functions #336

v2.4.0 - 2023-06-02

Pipeline Updates

• Updated template to nf-core/tools v2.8
• Add --bamqc_regions_file parameter for targeted methylation sequencing data #302
• ✨ Add NF-TEST tests and snapshots for the pipeline test profile #310

Bug fixes & refactoring

• 🛠️ update index file channels to explicit value channels #310
• 🐛 fix params.test_data_base in test and test_full configs #310
• 🤖 GitHub Actions CI - pull_request to dev tests with NXF_VER latest-everything #310
• 🤖 GitHub Actions CI - pull_request to master tests with NXF_VER 22.10.1 & latest-everything #310
• 🤖 GitHub Actions CI - fail-fast set to false #310
• 🐛 get to the bottom of index tests #278
• ✨ Support for Bismark methylation extraction ignore and ignore_3prime parameters when ignore_r1 or ignore_3prime_r1 are greater than 0. #322
• 🛠️ rename ignore -> ignore_r1 and ignore_3prime -> ignore_3prime_r1 params #322
• 🐛 fix ignore_3prime_r2 param #299
• 🐛 removed unused directory #297

v2.3.0 - 2022-12-16

Pipeline Updates

• ⚙️ Dramatically increase the default process time config requests for Bismark and bwa meth alignment
• ✨ Add a tower.yml file to enable Reports in Nextflow Tower
• 🤖 GitHub Actions CI - download the test data prior to running tests

Bug fixes & refactoring

• 🧹 Refactor genome indices preparation into a separate workflow
• 🧹 Refactor subworkflow logic out of alignment subworkflows, for later sharing
• 🐛 Fix a bug with using a local genome reference FASTA file
• 🐛 Fix a bunch of problems in the CI tests using nf-test (#279)

v1.0 - 2018-04-17

Version 1.0 marks the first release of this pipeline under the nf-core flag. It also marks a significant step up in the maturity of the workflow, with everything now in a single script and both aligner workflows fully supported.

• Renamed and moved SciLifeLab/NGI-MethylSeq to nf-core/methylseq
• Merged bwa-meth and bismark pipeline scripts, now chosen with --aligner flag
• Refactored multi-core parameters for Bismark alignment and methylation extraction
• Rewrote most of the documentation
• Changed the Docker container to use Bioconda installations

Previous to these releases, this pipeline was called SciLifeLab/NGI-MethylSeq: