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nf-core/cutandrun v1.1 Brass Viper
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@chris-cheshire chris-cheshire released this 20 Jan 11:08
· 758 commits to master since this release
1.1
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Learn about vigilant mode.

[1.1] - 2022-01-20

Enhancements & fixes

  • Updated pipeline template to nf-core/tools 2.2
  • [#71] - Bumped Nextflow version 21.04.0 -> 21.10.3
  • Added pipeline diagram to [README]
  • Upgraded all modules (local and nf-core) to support the new versioning system
  • The module getchromsizes was submitted to nf-core and moved from local to nf-core
  • Added support for GFF files in IGV session generation
  • [#57, #66] - Upgraded version reporting in multiqc to support both software version by module and unique software versions. This improves detection of multi-version software usage in the pipeline
  • [#54] - Fixed pipeline error where dots in sample ids inside the sample sheet were not correctly handled
  • [#75] - Fixed error caused by emtpy peak files being passed to the CALCULATE_FRIP and CALCULATE_PEAK_REPROD python reporting modules
  • [#83] - Fixed error in violin chart generation with cast to int64

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Old version New version
samtools 1.13 1.14

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

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