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@WackerO WackerO released this 31 Jan 12:36
· 322 commits to master since this release
2.1
64f7f63
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Learn about vigilant mode.

Added

  • #192 Added software_version yml functionality
  • #191 Added test software_versions.yml files for rsem and salmon
  • #188 Added titles to static heatmaps, added labels to static PCA plots
  • #176 Added output description to report
  • #175 Added nf-core citation to report
  • #173 Added GMT file to testdata dir to test #172
  • #172 Added option to provide custom gost GMT, for online gost, GMT is downloaded
  • #151 Added session info to report
  • #149 Added gene names to PA tables
  • #148 Added KEGG/REAC versions to report
  • #147 Added check for contrast list/metadata comparison
  • #145 Added pval threshold param
  • #136 Added pytest checks and md5sums to make sure that output stays consistent

Changed

  • #180 Bump version to 2.1 in some more files
  • #179 Release 2.1
  • #178 Bump version to 2.1
  • #177 Updated usage documentation
  • #174 Template update, changed param --metadata to --input
  • #169 Changed skip_pathway_analysis to run_pathway_analysis, default false
  • #165 -fw entries in multiqc stats are now merged
  • #164 Boxplots are now only generated for contrasts in list/matrix file if provided
  • #163 Template update, re-added limma, annotationdbi, colorbrewr to env (were previously incorrectly deleted), switched container to mamba
  • #159 Changed error messages for non-existing rsem/salmon files
  • #151 PCA plots and heatmap are now interactive, volcano and enrichment plots are cleaned up in their layout
  • #145 Renamed versions to software_versions

Fixed

  • #188 Fixed cut-off enrichment legends and cut-off volcano ylabs
  • #181 Fixed nf-core version test in ci.yml, updated schema.yml
  • #167 Corrected 5sum for batcheffect after container update
  • #152 Fixed empty qlist for gost query

Removed

  • #150 Removed human and mouse db from env.yml, both are now installed during pipeline execution if needed
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