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Published June 18, 2021 | Version 3.2
Software Open

nf-core/rnaseq: nf-core/rnaseq v3.2 - Copper Flamingo

Creators

  • 1. The Francis Crick Institute
  • 2. Science for Life Laboratory
  • 3. Boehringer Ingelheim
  • 4. @czbiohub
  • 5. Medical University of Innsbruck
  • 6. Inivata
  • 7. CZ BioHub
  • 8. @qbicsoftware
  • 9. Harvard Chan School of Public Health
  • 10. QBiC
  • 11. @SciLifeLab | Karolinska Institutet
  • 12. @maizeumn
  • 13. QBiC @qbicsoftware
  • 14. University College London
  • 15. @ScilifelabDataCentre
  • 16. Seqera Labs

Description

[3.2] - 2021-06-18 Enhancements & fixes

  • Removed workflow to download data from public databases in favour of using nf-core/fetchngs
  • Added a stand-alone Python script bin/fastq_dir_to_samplesheet.py to auto-create samplesheet from a directory of FastQ files
  • Added docs about overwriting default container definitions to use latest versions e.g. Pangolin
  • [#637] - Add --salmon_quant_libtype parameter to provide the --libType option to salmon quantification
  • [#645] - Remove trailing slash from params.igenomes_base
  • [#649] - DESeq2 fails with only one sample
  • [#652] - Results files have incorrect file names
  • [nf-core/viralrecon#201] - Conditional include are not expected to work
Parameters Old parameter New parameter --public_data_ids --skip_sra_fastq_download --salmon_quant_libtype

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present.

Files

nf-core/rnaseq-3.2.zip

Files (5.5 MB)

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Additional details

Related works

Is supplement to
https://github.com/nf-core/rnaseq/tree/3.2 (URL)