Skip to content

Wallace Chrysalis

Choose a tag to compare

View all tags
@sateeshperi sateeshperi released this 04 Jul 06:51
· 160 commits to master since this release
4.0.0
f3e4b1b
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

nf-core/methylseq v4.0.0 Release Notes

This release introduces major new features, significant refactoring, and extensive test suite improvements. Key highlights include the addition of a targeted sequencing analysis workflow, substantial refactoring of input handling and subworkflows for better modularity and robustness, and a complete overhaul of the testing framework.

Bug Fixes & Refactoring

  • Core Refactoring (#539):
    • The FASTA index subworkflow was refactored to remove implicit parameter passing.
    • Fixed workflow versions collection and improved conditional logic for FastQC and MultiQC execution.
  • Parabricks Fixes:
    • The minimum memory for PARABRICKS_FQ2BAMMETH has been increased to 100GB as suggested by the documentation (#528).
    • Fixed a parabricks/fq2bammeth failure on AWS Batch-like executors where symlinks don't exist (#536).
  • General:
    • Reverted PR #523 which involved direct changes to subworkflows in the pipeline.
    • The pipeline template has been updated to nf-core/tools v3.2.0 (#504).
    • The pipeline template has been updated to nf-core/tools v3.3.1 (#504).

Pipeline Updates

  • Targeted Sequencing (#516, #539):
    • A new --run_targeted_sequencing flag has been added to enable further analysis of targeted methylation experiments.
    • A new Targeted Sequencing subworkflow has been introduced with improved parameter handling and region-specific analysis capabilities.
    • The bedtools/intersect and picard/collecthsmetrics modules from nf-core/modules have been installed.
    • A new --collecthsmetrics parameter has been added to allow the collection of Picard HS metrics.
  • Workflow & Parameter Changes:
    • Bwameth:
      • Added --all_contexts and --merge_context parameters (#516).
      • Removed the --comprehensive parameter (#516).
    • Bismark:
      • Decoupled --merge_non_CpG from --comprehensive in the Bismark workflow (#516).
    • Trimming:
      • Added a new skip_trimming_presets flag to overwrite any preset trimming options (#506).
      • Updated --pbat trimming options to 8|8|8|8 (#506).
      • Removed --cegx and --epignome preset trimming options as the kits are discontinued (#506).
    • GPU Usage:
      • Removed the --use_gpu parameter. Activating the gpu profile with --profile gpu is now the standard way to enable GPU-based pathways (#520).
    • Quality Control:
      • Added --skip_fastqc and --skip_multiqc parameters to allow skipping quality control steps (#539).

Testing Updates (#539)

  • Test Suite Consolidation:
    • Removed 19 individual test files, replacing them with comprehensive test suites.
  • New Test Suites:
    • bismark_variants.nf.test for comprehensive Bismark testing.
    • bismark_hisat_variants.nf.test for Bismark with HISAT2 aligner.
    • bwameth_variants.nf.test for comprehensive Bwameth testing.
    • targeted_sequencing_variants.nf.test for the new targeted sequencing workflow.
    • index_downloads.nf.test for testing index download scenarios.

What's Changed

New Contributors

Full Changelog: 3.0.0...4.0.0

Contributors

lpantano, fbnrst, and 4 other contributors
Assets 2
Loading