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2.1.0 - 2022/07/12
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@rannick rannick released this 12 Jul 14:15
· 825 commits to master since this release
2.1.0
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Learn about vigilant mode.

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
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