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CHANGELOG.md

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nf-core/rnavar: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[1.1.0dev] nfcore/rnavar

Added

  • Addedunzip from nf-core modules for working with unzipped fasta and gtf files

Changed

  • #95 - Template update from nf-core/tools 2.5 -> 2.9
  • #97 - Template update from nf-core/tools 2.10
  • #109 - Update all modules
  • #111 - Template update from nf-core/tools 2.11
  • #117 - Template update from nf-core/tools 2.11.1

Fixed

  • #97 - Update all gatk4 modules to disable JVM hotspot
  • #124 - Fixed s3 bucket path in conditional statement for SnpEff cache
  • #127 - Fixed s3 bucket path in conditional statement for VEP cache

Dependencies

Dependency Old version New version
bcftools 1.17 1.18
bedtools 2.31.0 2.31.1
fastqc 0.11.9 0.12.1
mosdepth 0.3.3 0.3.6
multiqc 1.15 1.18
samtools 1.17 1.18

[1.0.0] nfcore/rnavar - 2022/06/20

First production release of the pipeline with latest software versions.

This version is based on GATK4 best-practices for RNAseq Ref and it includes:

Added

  • Added FastQC v0.11.9 from nf-core modules for read-level QC and summary.
  • Added STAR v2.7.9a from nf-core modules for read alignment to reference genome.
  • Added Samtools v1.15.1 from nf-core modules for alignment statistics and QC.
  • Added GATK v4.2.6.1 from nf-core modules for alignment post-processing, variant calling and filtration.
  • Added Tabix v1.11 from nf-core modules for indexing BAM ann VCF files.
  • Added SnpEff v5.0 from nf-core modules for variant annotation.
  • Added Ensembl VEP v104.3 from nf-core modules for variant annotation.
  • Added MultiQC v1.12 from nf-core modules for QC summary report.
  • Added Scatter i.e., one interval-list into many interval-files to run multiple processes in parallel.

Thanks to everyone that contributed to this release. Special thanks to @maxulysse and @FriederikeHanssen for your review and valuable suggestions.