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Dev -> master for v1.2.0#112

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pinin4fjords merged 90 commits intomasternf-core/differentialabundance:masterfrom devnf-core/differentialabundance:devCopy head branch name to clipboardApr 19, 2023

+828-225

Commits

Commits on Mar 3, 2023

• Bump versions after 1.1.1 bugfix release

  

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• Merge pull request #92 from healx/v1.1.1_post_release

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Commits on Mar 22, 2023

• make color palette specific to variables under consideration

  

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• Actually use dendrocolorscale

  

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• Update CHANGELOG

  

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• Exit workflow if gene sets not supplied for GSEA

  

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• Update changelog

  

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• dummy commit for CI

  

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• exits -> exceptions

  

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• Add reviewer to CHANGELOG

  

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Commits on Mar 23, 2023

• Bump shinyngs version used for notebook

  

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• Run prettier

  

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• throw -> error()

  

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• Correct CHANGELOG formatting

  

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• Bump shinyngs modules

  

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• Bump shinyngs again in markdown

  

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• Merge pull request #96 from healx/warn_missing_gene_sets

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• Merge branch 'dev' into more_color_scale_fixes

  

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Commits on Mar 24, 2023

• Merge pull request #94 from healx/more_color_scale_fixes

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Commits on Mar 28, 2023

• Update differential module interface, add pre-contrast subsetting options

  

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• Update CHANGELOG

  

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• Appease eclint

  

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• Merge pull request #103 from healx/subset_for_differential

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• Enabled multiple GMT/GMX files for GSEA

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Commits on Mar 29, 2023

• Update nextflow_schema.json

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• Update workflows/differentialabundance.nf

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• Update workflows/differentialabundance.nf

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• Update workflows/differentialabundance.nf

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• Update conf/modules.config

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• Update workflows/differentialabundance.nf

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• Update assets/differentialabundance_report.Rmd

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• Update conf/modules.config

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• Update assets/differentialabundance_report.Rmd

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Commits on Mar 30, 2023

• Merge branch 'dev' of https://github.com/nf-core/differentialabundance into multi_gmt

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• Updated changelog, bugfix

  WackerO

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  e5e35bf

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• still trying to figure out unreproducible github bug

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  b4caa83

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• still trying to figure out unreproducible github bug

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  b6c5447

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• Corrected modules.config

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Commits on Mar 31, 2023

• Add new reporting params

  

  Jonathan Manning

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• Merge pull request #105 from WackerO/multi_gmt

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• Add and wire in the shinyngs app generation

  

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• Merge branch 'dev' into add_shinyngs_app

  

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  7e490aa

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• Update CHANGELOG

  

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• Appease eclint

  

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• Update docs

  

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• Add shinyngs/shinyapps.io params

  

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• Shiny app generation should be conditional

  

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• appease eclint

  

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• update subway map

  

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• run prettier

  

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• Add missing descriptions

  

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• Temporarily eactivate app building for arrays

  

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• Module updates

  

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• Mix in versions for shinyngs app

  

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• Pass assay names

  

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• Fix modules conf

  

  Jonathan Manning

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• --diff_feature_id_col not valid yet

  

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Commits on Apr 3, 2023

• Use final assay to flag stats-associated assay for shinyngs

  

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Commits on Apr 4, 2023

• Tweak app module ahead of proper bump

  

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• Add reporting screenshots to README

  

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• Add log guessing for app

  

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Commits on Apr 5, 2023

• Improve shiny docs

  

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• Pretter docs

  

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Commits on Apr 7, 2023

• Bump modules

  

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• Remove workaround no longer necessary

  

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• Apply non-shinyngs module updates

  

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• Bump shinyngs in markdown too

  

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Commits on Apr 8, 2023

• install shinyngs modules properly after modules PR

  

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• install shinyngs modules properly after modules PR

  

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• Revert "install shinyngs modules properly after modules PR"

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• Renable app generation for affy arrays now there's a fix upstream

  

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• Remove function moved upstream

  

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• patch while we wait for pinin4fjords/shinyngs#44 to release upstream

  

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Commits on Apr 9, 2023

• Add reviewer

  

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• Wire in markdown report to app generation

  

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• Revert "Wire in markdown report to app generation"

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Commits on Apr 10, 2023

• Merge pull request #107 from healx/add_shinyngs_app

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Commits on Apr 18, 2023

• Add shiny app outputs to Tower reports

  

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• Update changelog

  

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• dummy commit

  

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Commits on Apr 19, 2023

• Add reviewers to changelog

  

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• Fix changelog formatting

  

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• Merge pull request #110 from healx/shinyngs_tower_yml

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• Pre-release changes for 1.2.0

  

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• Dummy commit after PR base fix

  

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• fix version indent

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• Merge pull request #111 from healx/release_v1.2.0

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• Fix typos

  

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• Dummy commit for CI

  

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• Merge pull request #113 from healx/pre_v1.2.0_fixes

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