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v 2.0.0 - 2022-05-31 Aqua Zinc Chihuahua

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@apeltzer apeltzer released this 31 May 19:24
· 1063 commits to master since this release
d1299b1

v2.0.0 - 2022-05-31 Aqua Zinc Chihuahua

Major enhancements

  • Updated pipeline template to nf-core/tools 2.4.1
  • [#137] - Update mirtop container to version 0.4.25 to fix multiqc error
  • Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
  • Bump minimum Nextflow version from 20.04.0 -> 21.10.3
  • Point to the proper test data branch
  • Software version(s) will now be reported for every module imported during a given pipeline execution
  • Updated nextflow_schema.json should now display correctly on Nextflow Tower
  • Added mirtop logs to multiqc
  • Allow a gene to be associated to a non null number of reads in all samples (in edgeR_miRBase.r script)

Other enhancements & fixes

  • #134 - Fixed colSum of zero issues for edgeR_miRBase.R script
  • #55 - update seqcluster to fix UMI-detecting bug

Parameters

Old parameter New parameter
--conda --enable_conda
--clusterOptions

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.

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
bioconductor-edger 3.26.5 3.36.0
bioconductor-limma 3.40.2 3.50.0
mirdeep2 2.0.1.2 2.0.1.3
mirtop 0.4.23 0.4.25
multiqc 1.10.1 1.12.0
python 3.7.3 3.8.3
r-base 3.6.3 4.0.3
r-data.table 1.12.4 1.14.2
r-gplots 3.0.1.1 3.1.1
r-statmod 1.4.32 1.4.36
samtools 1.12 1.13
seqcluster 1.2.7 1.2.9
seqkit 0.16.0 2.0.0
trim-galore 0.6.6 0.6.7
bioconvert - 0.4.3
htseq - -
markdown - -
pymdown-extensions - -
pygments - -
r-r.methodss3 - -

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.

What's Changed in terms of PRs

New Contributors

Full Changelog: 1.1.0...2.0.0