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Dev ratio fix channels#336

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suzannejin wants to merge 194 commits intonf-core:masternf-core/differentialabundance:masterfrom suzannejin:dev-ratio-fix-channelssuzannejin/differentialabundance:dev-ratio-fix-channelsCopy head branch name to clipboard

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Commits

Commits on May 8, 2024

• Template update for nf-core/tools version 2.14.0

  nf-core-bot

  committed
  f7dabe4

Commits on May 9, 2024

• Template update for nf-core/tools version 2.14.1

  nf-core-bot

  committed
  41729bc

Commits on May 22, 2024

• Update differentialabundance_report.Rmd

  pinin4fjords

  authored
  d604128

• Update CHANGELOG.md

  pinin4fjords

  authored
  20a44d6

• Update CHANGELOG.md

  pinin4fjords

  authored
  c05522a

• Merge branch 'TEMPLATE' of https://github.com/nf-core/differentialabundance into template_up2_14_1

  WackerO

  committed
  e8b0e58

• prettier

  WackerO

  committed
  e623b0d

• Merge pull request nf-core#273 from WackerO/template_up2_14_1

  Show description for cc7b3e0
  WackerO

  authored
  cc7b3e0

• fix files_unchanged

  pinin4fjords

  committed
  ab26e4c

• Merge branch 'dev' into more_than_10_contrasts

  pinin4fjords

  committed
  62c5146

• Update CHANGELOG.md

  pinin4fjords

  authored
  bcfde26

• Merge pull request nf-core#272 from nf-core/more_than_10_contrasts

  Show description for 4986420
  pinin4fjords

  authored
  4986420

Commits on May 24, 2024

• Fix pagination on samples tableee

  pinin4fjords

  authored
  dadf5db

• Update CHANGELOG.md

  pinin4fjords

  authored
  04635ef

• Fix CHANGELOG

  pinin4fjords

  committed
  8353e97

• Reset versions after release

  pinin4fjords

  committed
  2d1f602

• Fix linting

  pinin4fjords

  committed
  349273f

• Merge pull request nf-core#274 from nf-core/fix_pagination

  Show description for 5ddc8dd
  pinin4fjords

  authored
  5ddc8dd

Commits on Jun 13, 2024

• bugfix for gprofiler without gene_sets

  WackerO

  committed
  925527d

• add comment, update changelog

  WackerO

  committed
  ccb9aa4

Commits on Jun 14, 2024

• simplified gene_sets logic

  WackerO

  committed
  af2436f

• Merge pull request nf-core#278 from WackerO/fix_gpro_genesets

  Show description for 2dce45a
  WackerO

  authored
  2dce45a

Commits on Jun 25, 2024

• bump_shinyngs

  pinin4fjords

  committed
  4c608da

• Wire in new shinyngs log options, remove deprecated guessing option

  pinin4fjords

  committed
  2ab83e7

• Fix contrast specification to app creation

  pinin4fjords

  committed
  57574cf

• Can install from master now

  pinin4fjords

  committed
  b7af68a

• Update CHANGELOG

  pinin4fjords

  committed
  8fb05ca

• Merge pull request nf-core#280 from nf-core/bump_shinyngs

  Show description for 03b7984
  pinin4fjords

  authored
  03b7984

Commits on Jul 18, 2024

• add propr, mygene and fiter_var module

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  eff2e81

• add functional subworkflows into subworkflows/local

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  708c4db

• add schema_tools and tools_samplesheet to assets

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  4a76cef

• add crg.config and modules.config (as modules_coda) to conf

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  93ae92d

• add main.nf as main_coda.nf

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  da30859

• add nextflow.config and nextflow schema as nextflow_coda and nextflow_schema_coda

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  7487789

• add YMC counts and samplesheet to help for testing

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  a91626b

• upload mygene module with nf-core module install

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  6f8d5b0

• fix linting errors

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  969d15a

• solve remaining lint erros

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  a2d3824

• update propr/grea with nf-core modules install

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  b59f668

• modify propr main.nf to match nf-core repository

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  45b776e

• install propd with nf-core modules install

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  d60f031

• fix pre-commit errors in .json files

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  8b25351

• install propr/propr with nf-core modules install

  

  Cristina Araiz

  authored and

  Cristina Araiz

  committed
  fc123ec

• Merge pull request nf-core#281 from caraiz2001/dev-ratio

  Show description for bf70167
  caraiz2001

  authored
  bf70167

Commits on Jul 26, 2024

• small fixes to allow main_coda.nf to run

  

  bjlang

  committed
  e3fde5b

• Allow caching for -resume

  

  bjlang

  committed
  d45c4aa

• Allow caching for -resume

  

  bjlang

  committed
  b8221e3

• Use recommended format for optional parameters

  

  bjlang

  committed
  83b8fdc

• Use recommended format for optional parameters

  

  bjlang

  committed
  20c6cc6

• Skip copying matrix if not necessary to allow resuming pipeline execution

  

  bjlang

  committed
  b719387

Commits on Jul 29, 2024

• Skip copying matrix if not necessary to allow resuming pipeline execution

  

  bjlang

  committed
  5a3727b

Commits on Jul 30, 2024

• Update CHANGELOG.md

  

  bjlang

  committed
  0fbdcd6

• Keep original matrix file name in the annotation copy to improve resumability

  

  bjlang

  committed
  124f21e

• Update CHANGELOG.md

  Show description for 0e6b4fc
  

  bjlang

  and

  WackerO

  authored
  0e6b4fc

• Keep original matrix file name in the annotation copy to improve resumability

  

  bjlang

  committed
  0a3927a

Commits on Jul 31, 2024

• Merge pull request nf-core#282 from bjlang/dev

  Show description for c44e6bc
  WackerO

  authored
  c44e6bc

Commits on Aug 27, 2024

• Move main_coda logic into differentialabundance as experimental study type

  

  bjlang

  committed
  05cfb3a

• Merge pull request nf-core#284 from nf-core/dev

  Show description for 5e5c6e4
  bjlang

  authored
  5e5c6e4

• Merge branch 'nf-core:dev-ratio' into dev-ratio

  bjlang

  authored
  718075b

• Do not put not not in the not wrong place!

  

  bjlang

  committed
  b218940

• Merge branch 'dev-ratio' of https://github.com/bjlang/differentialabundance into dev-ratio

  

  bjlang

  committed
  3a69aae

• Merge pull request nf-core#283 from bjlang/dev-ratio

  Show description for 6e6a740
  bjlang

  authored
  6e6a740

Commits on Sep 3, 2024

• - use validated input for experimental workflow

  Show description for 04abe25
  

  bjlang

  committed
  04abe25

• Merge branch 'nf-core:dev-ratio' into dev-ratio

  bjlang

  authored
  2fe78de

• small fix

  

  bjlang

  committed
  3254d25

• Merge branch 'dev-ratio' of https://github.com/bjlang/differentialabundance into dev-ratio

  

  bjlang

  committed
  d133c6d

Commits on Sep 6, 2024

• Add CoDA/experimental branch to CI tests

  

  bjlang

  committed
  8fcc24c

• fix linting

  

  bjlang

  committed
  9532cfb

• fix testing parameters

  

  bjlang

  committed
  318706a

Commits on Sep 10, 2024

• Merge pull request nf-core#285 from bjlang/dev-ratio

  Show description for 9421df1
  bjlang

  authored
  9421df1

Commits on Sep 13, 2024

• Delete conf/crg.config

  bjlang

  authored
  b71b83e

Commits on Sep 20, 2024

• minor code restructuring

  

  bjlang

  committed
  4a41e66

• Merge pull request nf-core#290 from bjlang/dev-ratio

  Show description for 293b30e
  bjlang

  authored
  293b30e

Commits on Oct 1, 2024

• Store output of different pathways in different folders

  

  bjlang

  committed
  a6c2b3d

Commits on Oct 2, 2024

• within differential subworkflow, initialize results channels at the beginning. Then the results from each process can be mixed accordingly

  suzannejin

  committed
  a0ef41b

• formatting

  suzannejin

  committed
  ca6fb97

• removed the variable selection block between diff and corr blocks.

  suzannejin

  committed
  328aacd

• updated toolsheet to the current experimental workflow status

  suzannejin

  committed
  f4c4d2f

• formatting

  suzannejin

  committed
  3160a09

• remove trailing spaces

  suzannejin

  committed
  c9b9482

• updated schema_tools.json

  suzannejin

  committed
  fc95675

• remove filtervar related modules and subworkflows.

  suzannejin

  committed
  7bc6ee8

Commits on Oct 3, 2024

• updated modules.config with the correct nomenclature for grea

  suzannejin

  committed
  283385a

Commits on Oct 7, 2024

• Merge pull request nf-core#293 from suzannejin/dev-ratio

  Show description for 25ace61
  suzannejin

  authored
  25ace61

• added new version propd

  suzannejin

  committed
  aac7085

Commits on Oct 8, 2024

• remove old container comment

  suzannejin

  committed
  ecfc184

• added comment to propd.R

  suzannejin

  committed
  6885bfd

• trim trailing spaces

  suzannejin

  committed
  b7a2774

• [automated] Fix code linting

  nf-core-bot

  committed
  8c75e55

• prettier modules.json

  suzannejin

  committed
  c36e237

• Merge branch 'dev-ratio' of https://github.com/suzannejin/differentialabundance into dev-ratio

  suzannejin

  committed
  ed06869

• add more tests to experimental

  suzannejin

  committed
  1731b3d

• modify propd.R to not erroring when no FDR cutoff is found

  suzannejin

  committed
  36868e1

• add comment

  suzannejin

  committed
  c5ddf64

• Template update for nf-core/tools version 3.0.0

  nf-core-bot

  committed
  c1b8817

• test_experimental also run propd_fdr

  suzannejin

  committed
  c74c341

• also get ch_results_genewise from propd

  suzannejin

  committed
  879b8a7

• added local module propr/propr

  suzannejin

  committed
  1696e1c

• fix bug in propr.R

  suzannejin

  committed
  bc9c86a

• remove nf-core/propr/grea

  suzannejin

  committed
  fed6d45

• add local propr/grea module

  suzannejin

  committed
  cf58a2b

• modified enrichment subworkflow to fit new grea module

  suzannejin

  committed
  5b56162

• fix bug in enrichment.nf

  suzannejin

  committed
  38a32b6

Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

  nf-core-bot

  committed
  5626dc7

Commits on Oct 10, 2024

• added updated local version of propr/grea module

  suzannejin

  committed
  118b257

• change test_experimental to remove propd_grea (no container yet)

  suzannejin

  committed
  5c44e3c

• Merge pull request nf-core#296 from suzannejin/dev-ratio

  Show description for f8811e4
  suzannejin

  authored
  f8811e4

Commits on Oct 11, 2024

• Skip fastqc, igenomes and nf_schema

  pinin4fjords

  committed
  995a656

• Update CHANGELOG

  pinin4fjords

  committed
  d719fca

• [automated] Fix code linting

  nf-core-bot

  committed
  3e5cda8

• Merge pull request nf-core#299 from nf-core/add_exclusions

  Show description for 19491be
  mashehu

  authored
  19491be

• fix structure of .nf-core.yml

  mashehu

  committed
  2f1a540

• Merge pull request nf-core#300 from nf-core/fix-nf-core.yml

  Show description for 2222062
  mashehu

  authored
  2222062

• Template update for nf-core/tools version 3.0.1

  nf-core-bot

  committed
  b498163

• Template update for nf-core/tools version 3.0.2

  nf-core-bot

  committed
  4446eab

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

  pinin4fjords

  committed
  7ddbed7

• Linting fixes

  pinin4fjords

  committed
  488f1a2

• Fix linting

  pinin4fjords

  committed
  2d0ebac

• Fix files_unchanged

  pinin4fjords

  committed
  c57a3c0

• Linting fixes

  pinin4fjords

  committed
  5bb2b16

• Fix template pngs

  pinin4fjords

  committed
  4cde832

• skip exists check for multiqc config

  pinin4fjords

  committed
  f56e710

• Fix action

  pinin4fjords

  committed
  75b5f79

• correct skipping

  pinin4fjords

  committed
  1c7ad9d

• correct skipping

  pinin4fjords

  committed
  cdb7f44

• remove lingering check_max

  pinin4fjords

  committed
  4db87df

• Fix multiqc config

  pinin4fjords

  committed
  8336577

• Merge pull request nf-core#303 from nf-core/merging-template-updates

  Show description for 83699b7
  pinin4fjords

  authored
  83699b7

Commits on Oct 14, 2024

• Merge branch 'dev' into dev-ratio

  pinin4fjords

  authored
  e977214

Commits on Oct 16, 2024

• added the params for experimental workflow

  suzannejin

  committed
  46f1d8e

• udpate schema for tools

  suzannejin

  committed
  e8f159a

• updated fromSamplesheet to samplesheetToList

  suzannejin

  committed
  36fcff4

• set toolsheet schema

  suzannejin

  committed
  66148af

• remove temporal config

  suzannejin

  committed
  576bb8c

• minor changes

  suzannejin

  committed
  59bd17c

• fix error related to .nf-core.yml

  suzannejin

  committed
  bd51d59

• properly set the resources limits for test_experimental.config

  suzannejin

  committed
  a077c03

Commits on Oct 17, 2024

• update propd.R template to compute weighted connectivity for hub genes

  suzannejin

  committed
  d7ab1ca

• add parameter for propd_weighted_degree

  suzannejin

  committed
  9819e84

Commits on Oct 18, 2024

• updated propr container

  suzannejin

  committed
  b566842

• modify propd.R so that it output some plots for the top red/yellow/green pairs

  suzannejin

  committed
  ab9587b

Commits on Oct 22, 2024

• Merge pull request nf-core#302 from suzannejin/dev-ratio

  Show description for aa03e1a
  suzannejin

  authored
  aa03e1a

• Merge branch 'dev-ratio' of https://github.com/bjlang/differentialabundance into dev-ratio

  

  bjlang

  committed
  95e406a

• finish merge

  

  bjlang

  committed
  0464932

• Split toolsheet data into subworkflow dedicated channels

  

  bjlang

  committed
  41adc93

• Fix linting and include propd_grea in test

  

  bjlang

  committed
  1cbdb17

Commits on Oct 23, 2024

• remove duplicate tools declaration

  

  bjlang

  committed
  9d35597

• Temporarily remove pathway from meta to run processes only once per data/argument combination

  

  bjlang

  committed
  062c5a3

• fix typo

  

  bjlang

  committed
  4075a80

• Merge pull request nf-core#308 from bjlang/dev-ratio

  Show description for a594ebf
  bjlang

  authored
  a594ebf

• Move pathway related logic out of differential and correlation SWF

  

  bjlang

  committed
  f4e8164

• Merge branch 'nf-core:dev-ratio' into dev-ratio

  bjlang

  authored
  74c77bd

Commits on Oct 24, 2024

• fix bug with number_of_cutoffs in propd.R

  suzannejin

  committed
  bd7d5d4

Commits on Oct 25, 2024

• update toolsheet

  suzannejin

  committed
  8db59cc

• updated propr container and modified propd.R to loop through FDR testing when no meaningful cutoff is found

  suzannejin

  committed
  dab58e5

• Merge pull request nf-core#320 from suzannejin/dev-ratio-propd-loop

  Show description for 3c8be72
  suzannejin

  authored
  3c8be72

Commits on Oct 28, 2024

• shorten test_experimental into the essential tests

  suzannejin

  committed
  094452b

• Merge branch 'dev-ratio' into dev-ratio-plot-exploratory

  suzannejin

  authored
  14b625b

• trim trailing

  suzannejin

  committed
  e345168

• Merge pull request nf-core#324 from suzannejin/dev-ratio-plot-exploratory

  Show description for 0329206
  suzannejin

  authored
  0329206

• Modify differential/main.nf to include limma

  syangaskhan

  committed
  af86bb2

Commits on Oct 29, 2024

• modify limma input

  suzannejin

  authored
  aca5f24

• modify limma input

  suzannejin

  authored
  afd7522

• trim trailing

  suzannejin

  authored
  e8067ac

• Merge pull request nf-core#328 from syyang93/limma_add

  Show description for 1f4e926
  suzannejin

  authored
  1f4e926

• add limma to test_experimental

  suzannejin

  committed
  4477e1c

• add filtering step for limma

  suzannejin

  committed
  898af43

• fix bug

  suzannejin

  committed
  c6db7ff

• change filter_difftable_limma input column names

  suzannejin

  committed
  3b398ac

• add todo

  suzannejin

  committed
  f97ba6b

• Merge pull request nf-core#331 from suzannejin/dev-ratio-limma

  Show description for 1d5b909
  suzannejin

  authored
  1d5b909

• add GPROFILER2 module to ENRICHMENT subworkflow

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  f2b6322

• Once more reorganize the pathway logic

  

  bjlang

  committed
  94d3c8e

• Merge remote-tracking branch 'upstream/dev-ratio' into dev-ratio

  

  bjlang

  committed
  e5a5d15

• add new pathway_names to test gprofiler2

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  02a38bb

• run GPROFILER2 only when enr_method is specified in the ch_tools channel

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  067c592

• remove trailing whitespace

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  47bb659

• add new line at end of file

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  90001a2

• Adapt Limma call

  

  bjlang

  committed
  f7c5c77

Commits on Oct 30, 2024

• Merge pull request nf-core#333 from nf-core/323_add_module_gprofiler2

  Show description for 4889998
  suzannejin

  authored
  4889998

• Merge remote-tracking branch 'upstream/dev-ratio' into dev-ratio

  

  bjlang

  committed
  1198761

• Implement review comments

  

  bjlang

  committed
  953eb51

• add deseq2 pathway name

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  4a5aa60

• add DESEQ2 block to this workflow

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  3546cb0

• set nsub to lower numebr given nature of test data

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  ba1ea24

• resolve merge conflicts

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  d6da7ad

• fix linting

  

  Breeshey Roskams-Hieter

  authored and

  Breeshey Roskams-Hieter

  committed
  a2ddd8a

• update channel name to samples_and_matrix

  Show description for a282a47
  

  roskamsh

  and

  WackerO

  authored
  a282a47

• update channel name to samples_and_matrix

  Show description for 0e4a84d
  

  roskamsh

  and

  WackerO

  authored
  0e4a84d

• update channel name to samples_and_matrix

  Show description for a885116
  

  roskamsh

  and

  WackerO

  authored
  a885116

Commits on Nov 4, 2024

• Merge pull request nf-core#335 from nf-core/322_add_module_deseq2

  Show description for 0f9c9fc
  suzannejin

  authored
  0f9c9fc

• Merge pull request nf-core#318 from bjlang/dev-ratio

  Show description for 6d0d3b8
  suzannejin

  authored
  6d0d3b8

• fix the channels properly with the new preprocess/postprocess scheme for input/output channels

  suzannejin

  committed
  1cba7e6

• modify preprocess_subworkflow_input to filter the elements where method == []

  suzannejin

  committed
  2a1d9b2