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v2.0.0 - 2022/05/19
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@rannick rannick released this 19 May 11:22
· 975 commits to master since this release
2.0.0
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Learn about vigilant mode.

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
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