2.1.0 - 2022/07/12

IMPORTANT
Since STAR has been updated, a new STAR index needs to be built as reference.
nextflow run nf-core/rnafusion --genomes_base /PATH/TO/REFERENCES --starindex --build_references --outdir OUTDIR -profile singularity or docker

Added

• FusionCatcher single_end support for single reads ABOVE 130 bp
• --fusioninspector_only parameter to run FusionInspector standalone feeding gene list manually with parameter --fusioninspector_fusions PATH
• --fusioncatcher_limitSjdbInsertNsj parameter to feed --limitSjdbInsertNsj to FusionCatcher
• --fusioninspector_limitSjdbInsertNsj parameter to feed --limitSjdbInsertNsj to FusionInspector !!Any other value than default will use the dev version of FusionInspector!!
• OPTIONAL trimming option --trim for hard trimming to 75 bp in case of high read-through. Only fusioncatcher uses trimmed reads as STAR-based fusion detection tools are less sensitive to read-through
• picard metrics, STAR final log, and QualiMap output included in MultiQC report

Changed

• seq_platform and seq_center changed from boolean to string
• seq_platform set to an empty string and seq_center set to an empty string if not existing
• Arriba use ensembl references-built starindex independently of starfusion_build parameter
• ftp to http protocol for STARFUSION_BUILD process Pfam-A.hmm.gz download as ftp causes issues on some servers
• Updated README and usage documentation with more detailed information and metro map
• Arriba use ensembl references-built starindex independently of starfusion_build parameter
• Update of the single-end reads support table in README, added recommendation to use single-end reads only in last resort
• STAR updated to 2.7.10a
• Arriba updated to 2.3.0, references for blacklist and protein domains changed to 2.3.0 from singularity/docker container -> arriba download of references not necessary any more
• multiQC updated to 1.13a
• picard updated to 2.27.4
• dumpsoftwareversions module updated to use multiqc=1.12 containers

Fixed

• FusionInspector does not mix sample reads with fusion lists and meta information from other samples anymore
• Arriba visualisation does not mix sample reads with fusion lists and meta information from other samples anymore
• logging of STAR-fusion and fusionreport version

v2.0.0 - 2022/05/19

The usage of the pipeline has been updated. It is recommended to reads the usage.md document.

Added

• Added qualimap/rnaseq v2.2.2d from nf-core modules
• Added UCSC gtfToGenePred v377
• Added picard CollectRnaSeqMetrics v2.26.10
• Added picard MarkDuplicates v2.26.10 from nf-core modules
• Added cat/fastqc from nf-core modules
• Added possibility for manually feeding the results of fusions from different tools to speed-up reruns
• STAR-Fusion references can be downloaded or built but downloaded references are NOT RECOMMENDED as not thoroughly tested (--starfusion_build parameter is true by default, use --starfusion_build false to use downloaded STAR-Fusion references).

Changed

• Upgrade default ensembl version to 102
• Upgrade to nf-core/tools v2.3.2
• Upgrade Arriba v1.2.0 to Arriba v2.2.1
• Upgrade FusionCatcher v1.20 to FusionCatcher v1.33
• Upgrade STAR-fusion v1.8.1 to STAR-fusion v1.10.1
• Upgrade STAR v2.7.1 to STAR v2.7.9
• Upgrade fusion-report v2.1.3 to fusion-report v2.1.5
• Upgrade kallisto v0.44.0 to kallisto v0.46.2
• Upgrade fastqc v0.11.8 to fastqc v0.11.9
• Upgrade samtools v1.9 to samtools v1.15.1
• Upgrade arriba references from v1.2.0 to v2.1.0
• Upgrade fusioncatcher references from v98 to v102
• Use arriba (detect only), kallisto and STAR from nf-core modules
• Instead of separate script to build the references, added --build_references argument in the main --fasta argument is not required with --build_references and set by default to the ensembl references built in the detection workflow

Removed

• Ericscript tool
• GRCh37 support. Subdirectory with params.genome are removed
• Running with conda

nf-core/rnafusion:1.2.0

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

• Fusion gene detection tools:
  • Arriba v1.2.0
  • Ericscript v0.5.5
  • Fusioncatcher v1.20
  • Pizzly v0.37.3
  • Squid v1.5
  • STAR-Fusion v1.8.1
• Visualization tools:
  • Arriba v1.2.0
  • FusionInspector v2.2.1
• Other tools:
  • fusion-report v2.1.3
  • FastQ v0.11.8
  • MultiQC v1.7
  • STAR aligner v2.7.1a

Added

• Added social preview image #107
• Simplified running the pipeline, better documentation

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

nf-core/rnafusion:1.1.0

v1.1.0 - 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

nf-core/rnafusion:1.0.2

v1.0.2 - 2018/05/16

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

nf-core/rnafusion:1.0.1

v1.0.1 - 2018/04/06

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

nf-core/rnafusion:1.0

Initial release of nf-core/rnafusion 🎉

This is the first production release under nf-core flag previously under SciLifeLab/NGI-RNAfusion.

This version includes:

• 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 v1.0
  • FastQ v0.11.8
  • MultiQC v1.7
  • FusionGDB updated at 2019/01/23

Thanks to everyone that contributed to this release 💪
Special thanks go to @maxulysse, @alneberg, @ewels, @szilvajuhos and @apeltzer