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Release 1.5.0#256

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WackerO merged 226 commits intomasternf-core/differentialabundance:masterfrom devnf-core/differentialabundance:devCopy head branch name to clipboardMay 8, 2024

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Commits

Commits on Oct 31, 2023

• Added round param for all modules (currently active for proteus und gprofiler), added citations for gprofiler, added gprofiler section to report

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

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Commits on Nov 7, 2023

• Param rename, reordered Citations, changed gprofiler2 report heading, added report text if no enrichment found, added gprofiler2 params to report and nextflow schema

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• Added docs entry for gprofiler

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Commits on Nov 8, 2023

• Corrected some entries in the schema

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Commits on Nov 13, 2023

• integrated module changes

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Commits on Nov 14, 2023

• Added PI and contact params for report; added newline between report author and workflow version

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Commits on Nov 16, 2023

• Newly installed gprofiler2 module, enabled it in full test

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

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• added gprofiler to git

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• prettier

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• Added gpro to test.config

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Commits on Nov 17, 2023

• changing the workflow to make gprofiler run multiple times if several contrasts are investigated

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Commits on Nov 21, 2023

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

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Commits on Nov 23, 2023

• GOST module update

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Commits on Nov 27, 2023

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

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

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• Removed write statements, updated metro map

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• Corrected metro maps, uncommented error case in workflow, fixed spelling error in schema, added rds to GOST output

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• bump versions

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• Fix resource issues

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• update changelog

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• [automated] Fix linting with Prettier

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• Update changelog

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• Merge branch 'de_resources' of github.com:nf-core/differentialabundance into de_resources

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• Merge pull request #208 from nf-core/de_resources

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Commits on Nov 29, 2023

• Added filtered DE tables to output; add rounding after gprofiler2 PR is merged

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Commits on Nov 30, 2023

• Renamed round_digits to report_round_digits, excluded gsea from default report params

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

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• fixed schema, added icons to proteus and gprofiler2

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Commits on Dec 1, 2023

• Update affy/justrma to pull in timeout fix

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• Update changelog

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• Poke CI

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Commits on Dec 4, 2023

• update changelog

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• Merge pull request #210 from nf-core/include_affy_fix

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• Fix volcano plot legend

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Commits on Dec 5, 2023

• Update CHANGELOG

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• Merge pull request #213 from nf-core/fix_volcano_legend

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• Combined gprofiler with gsea section in report results; added short gsea docu; replaced gsea with gprofiler in test config (gsea is still tested in test_affy); moved round_digits and gene_sets to n…

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

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• Changed param name in two configs

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• Fixed some old params

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Commits on Dec 8, 2023

• added difftable filtering module, added short docu section for gsea, renamed params

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• Param renames, adapted workflow to do the correct checks; fixed a bug in the gprofiler2 module. It is now the same as that in my nf-core/modules PR but I still need to 'officially' install the upda…

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• Added gprofiler organism, updated metro maps

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• Uploaded slimmer SVG, fixed mistake in ifelse

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• Updated gprofiler

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• Reordered report param

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• removed empty line

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Commits on Dec 13, 2023

• adapted gprofiler2 report section to gsea, changed order of docu, added gprofiler and gsea in parallel to test_full, removed gprofiler from test, made gprofiler use a background by default

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• Removed prints

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

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• Renamed gene_sets param, updated gprofiler

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• Added final newline

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Commits on Dec 14, 2023

• Removed redundant code lines

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• Update modules/local/filter_difftable.nf

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• Merge branch 'add_gpro' of https://github.com/WackerO/differentialabundance into add_gpro

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• Fixed filter module, added gprofiler background docu

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• Removed token from full test

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• Updated gprofiler docu

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Commits on Dec 15, 2023

• Updated output docs

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Commits on Dec 18, 2023

• Added param for selectively running gprofiler2 without GMT

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• Streamline gene set conditionals, don't overwrite global gene sets channel for gprofiler

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Commits on Dec 19, 2023

• removed gprofiler mode

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• Merge branch 'add_gpro' of https://github.com/WackerO/differentialabundance into add_gpro, update gprofiler2

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• Template update for nf-core/tools version 2.11

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Commits on Dec 20, 2023

• Update workflows/differentialabundance.nf

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• Update docs/usage.md

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• Added .first() to gene sets for gprofiler, made error message more specific

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• prettier

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• Template update for nf-core/tools version 2.11.1

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Commits on Dec 21, 2023

• Merge pull request #199 from WackerO/add_gpro

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

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• Merge branch 'nf-core-template-merge-2.11.1' of https://github.com/nf-core/differentialabundance into nf-core-template-merge-2.11.1

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• Undid some unnecessary changes

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• reinstalled matrixfilter to fix linting

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• Update assets/multiqc_config.yml

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• prettier

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• Updated changelog

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• Merge pull request #219 from nf-core/nf-core-template-merge-2.11.1

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Commits on Jan 8, 2024

• Update shinyngs modules to address density plots issue

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• update CHANGELOG

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Commits on Jan 9, 2024

• Added rounds to numeric tables

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• Removed newline to rerun git tests

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Commits on Jan 10, 2024

• Bump module to correct GSEA CLS file creation

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• Update CHANGELOG

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• Merge pull request #221 from nf-core/bump_shinyngs_for_density

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• Merge branch 'dev' into tabulartogseacls_fieldcheck

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• Merge pull request #223 from nf-core/tabulartogseacls_fieldcheck

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Commits on Jan 11, 2024

• Update changelog

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• Merge pull request #222 from WackerO/round_report

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Commits on Jan 16, 2024

• Changed report contact info to a single param and added CSS for styling; updated docs

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

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• Linting, bugfixes

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Commits on Jan 18, 2024

• Added gene_id_col to DESEQ2_NORM modules.config entry

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Commits on Jan 23, 2024

• Changed contributor info from file to string param, simplified CSS and RMD code

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• Update changelog, prettier

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Commits on Jan 24, 2024

• Renamed variable

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Commits on Jan 27, 2024

• Update assets/differentialabundance_report.Rmd

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• Merge pull request #197 from WackerO/project_info

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• Template update for nf-core/tools version 2.12

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Commits on Jan 30, 2024

• Merge branch 'dev' into nf-core-template-merge-2.12

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Commits on Jan 31, 2024

• Fix linting

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• Linting in report.Rmd

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• Merge branch 'nf-core-template-merge-2.12' of https://github.com/nf-core/differentialabundance into nf-core-template-merge-2.12

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• More linting, changelog update

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• Fix prettier issues

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• Merge pull request #228 from nf-core/nf-core-template-merge-2.12

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• GSEA update

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• Mention missing dots in volcano plot, change rounding, turn off rounding by default

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• Merge pull request #231 from WackerO/dev

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• Changed 0 pval warning

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• Add note on scaling

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• extend scaling note

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• Prettier

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• Merge pull request #233 from nf-core/scaling_note

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• Template update for nf-core/tools version 2.13

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• Publish gsea reports

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• Update CHANGELOG.md

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• Reenabled default rounding

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• Merge branch 'TEMPLATE' of https://github.com/nf-core/differentialabundance into merging-template-updates

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• trying to fix some issues after conflict solving

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Commits on Feb 22, 2024

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• Bugfixing

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• Bugfixing; removed samplesheet definition from pipelineInitialization

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• Removed remaining custom_dumpsoftware references; removed prints and dumps; fixed versions.yml bug

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• Merge pull request #241 from WackerO/merging-template-updates

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

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

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• Merge pull request #232 from WackerO/volcano_round

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• Belatedly added NA options for matrixfilter to the pipeline

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• made proportion_not_na conditional

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Commits on Feb 28, 2024

• Merge pull request #244 from WackerO/matrixfilter_na

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• Merge branch 'TEMPLATE' of https://github.com/nf-core/differentialabundance into merging-template-updates

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• Merge pull request #250 from WackerO/merging-template-updates

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• Merge pull request #240 from nf-core/publish_gsea_reports

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