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@rannick rannick released this 13 Mar 17:57
· 580 commits to master since this release
2.2.0
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Learn about vigilant mode.

Version 2.0.0 includes stringtie in --all, a fastp trimming option, fixed for arriba references among other (see details below).

Important: the references need to be rebuilt.

Check usage.md for how to use the new options.

Detailed CHANGELOG:

Added

  • exitStatus 140 now part of the retry strategy
  • stubs to all local modules
  • --stringtie option added with StringTie v2.2.1 to detect splicing events. Not included in fusion-report or fusionInspector summaries. Included in the --all workflow
  • Generation of ribosomal RNA interval list with build_references and use it in picard CollectRnaMetrics
  • Add csv output to fusionreport
  • Trimming workflow using fastp: use trimmed reads for all tools
  • whitelist parameter to add custom fusions to the detected ones and consider the whole for the fusionInspector analysis
  • Compression to CRAM files for arriba, squid and starfusion workflows (fusioncatcher and pizzly do not produce SAM/BAM files, fusioninspector BAM files are too small to benefit from compression)
  • --qiagen option to download from QIAGEN instead of COSMIC (use QIAGEN user and password for cosmic_username and cosmic_passwd)
  • Bumped STAR genomegenerate time request for building as it was always crashing for most users
  • Fixed issue with arriba visualisation parameters #326

Changed

  • Test profiles unified under 'test' but if the references do not all need to be downloaded, run with -stub
  • Update CUSTOM_DUMPSOFTWAREVERSIONS to use multiqc version 1.13
  • Updated to nf-core template 2.7.2, with all module updates
  • MultiQC updated to 1.13a in process dumpsoftwareversion
  • Patch fusion-report version with fixed mittelman DB and DB extraction date written into software_version.yaml
  • Arriba references back to downloading with build_references instead of taking from container
  • Arriba visualisation now running with Arriba v2.3.0
  • Updated STAR-Fusion to 1.12.0

Fixed

  • AWS megatest to display on nf-core website
  • arriba visualisation references updated to 2.3.0
  • Removed issue with multiple outputs in samtools view for squid

Removed

  • FUSIONINSPECTOR_DEV process as the option fusioninspector_limitSjdbInsertNsj is part of the main starfusion release
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