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nfcore/rnafusion: Changelog

All notable changes to this project will be documented in this file.

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

[1.2.0] nfcore/rnafusion - 2020/07/15

Added

  • Added social preview image #107

Changed

  • Upgrade fusion-report v2.1.2 to fusion-report v2.1.3
  • Upgrade fusion-report v2.1.1 to fusion-report v2.1.2
  • Upgrade fusion-report v2.1.0 to fusion-report v2.1.1
  • Upgrade Arriba v1.1.0 to Arriba v1.2.0
  • Upgrade fusion-report v2.0.2 to fusion-report v2.1.0

Fixed

  • Missing strip-components in download-references.nf/star-fusion #148
  • Missing version prefix for cdna #143
  • samtools missing header in empty file for FusionInspector ref
  • Removed profile from helper scripts #139
  • Wrong url path for Pfam-A.hmm.gz #140

Removed

  • Removed scripts/download-singularity-img.sh and download-singularity-img.nf as they are not necessary any more

[1.1.0] nfcore/rnafusion - 2020/02/10

  • Fusion gene detection tools:
    • Arriba v1.1.0
    • Ericscript v0.5.5
    • Fusioncatcher v1.20
    • Pizzly v0.37.3
    • Squid v1.5
    • STAR-Fusion v1.6.0
  • Visualization tools:
    • Arriba v1.1.0
    • FusionInspector v1.3.1
  • Other tools:
    • fusion-report v2.0.1
    • FastQ v0.11.8
    • MultiQC v1.7
    • STAR aligner v2.7.0f

Added

  • Added Arriba 1.1.0 #63
  • Added Batch mode #54

Changed

  • Updated examples and configurations
  • Upgraded fusion-report v1.0.0 to fusion-report v2.0.1
  • Divided running_tools into fusion and visualization tools
  • Updated STAR in Squid, Fusion-Inspector version to 2.7.0f
  • Upgraded STAR-Fusion v1.5.0 to STAR-Fusion v1.6.0 #83
  • Parameter igenomesIgnore renamed to igenome #81
  • Finished STAR-Fusion file renaming #18
  • Updated logos
  • Updated to nf-core 1.8 TEMPLATE

Fixed

  • iGenomes optional, but not really #91
  • Updated fusioncatcher to latest 1.20 version also solving #95

Removed

  • Variables pizzly_fasta and pizzly_gtf have been removed and replaced with transcript and gtf
  • Jenkisfile, test configuration, pylintrc configuration
  • Removed igenomes.config because the pipeline only supports Ensembl version

[1.0.2] nfcore/rnafusion - 2019/05/13

Changed

  • Bumped nf-core template to 1.6 #69

Fixed

  • Fixed COSMIC parameters not wrapped in quotes #75
  • Implemented output output for fusion tools #72
  • Fixed reference download link for STAR-Fusion #71

[1.0.1] nfcore/rnafusion - 2019/04/06

Added

  • Added support for extra parameters for tools STAR-Fusion, FusionCatcher and fusion-report
  • Added example configuration for singularity and docker
  • Added fusion-report into the stack #62, #55, #53, #51
  • Added nextflow helper script download-singularity-img.nf
  • Added nextflow helper script download-references.nf
  • Added Jenkinsfile for in-house testing

Changed

  • Updated installation of FusionCatcher (available now on bioconda)

Fixed

  • Fixed empty symlinks (input.X) in fusion-report #68
  • Fixed FASTA issues #60
  • Fixed centralized nf-core/config #64
  • Fixed scrape_software_versions.py to parse tools versions correctly #65

Removed

  • Removed Singularity

[1.0] nfcore/rnafusion - 2018/02/14

Version 1.0 marks the first production release of this pipeline under the nf-core flag. The pipeline includes additional help scripts to download references for fusion tools and Singularity images.

  • Fusion gene detection tools:
    • STAR-Fusion v1.5.0
    • Fusioncatcher v1.00
    • Ericscript v0.5.5
    • Pizzly v0.37.3
    • Squid v1.5
  • Visualization tools:
    • FusionInspector v1.3.1
  • Other tools:
    • Summary report
    • FastQ v0.11.8
    • MultiQC v1.7
    • FusionGDB updated 2019/01/23

[0.1] SciLifeLab/NGI-RNAfusion (ARCHIVED) - 2018/10/05

Initial release of NGI-RNAfusion, created with the nf-core template. Source code can be found at SciLifeLab/NGI-RNAfusion. The solution works with Docker and Singularity.

  • Tools:
    • STAR-Fusion
    • Fusioncatcher
    • FusionInspector
    • Custom tool for fusion comparison - generates intersection of detected fusion genes from all tools