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Integrate subworkflows into pipeline #431

Merged
merged 61 commits into from
Feb 21, 2025
Merged

Integrate subworkflows into pipeline #431

merged 61 commits into from
Feb 21, 2025
+6,468 −1,025

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suzannejin
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@suzannejin
Squashed commit of the following:
a64d4d7 
commit 9e4a105
Merge: 8059211 128ffe8
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Dec 2 12:37:20 2024 +0100

    Merge pull request #329 from nf-core/311-add-module-gsea

    311 add module gsea

commit 128ffe8
Merge: 440e40f 8059211
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Fri Nov 15 16:34:38 2024 +0100

    Merge branch 'dev-ratio' into 311-add-module-gsea

commit 8059211
Merge: 6d0d3b8 13bc1b7
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Fri Nov 15 16:29:15 2024 +0100

    Merge pull request #357 from bjlang/dev-ratio

    Fix tests; add version channels; remove params access in subworkflow

commit 13bc1b7
Author: bjlang <>
Date:   Fri Nov 15 16:00:42 2024 +0100

    Fix DEseq2 call

commit 047099e
Author: bjlang <>
Date:   Fri Nov 15 15:46:26 2024 +0100

    Revert "Ensure ch_transcript_lengths and ch_control_features being channels and not arrayLists"

    This reverts commit 655ad61.

commit 655ad61
Author: bjlang <>
Date:   Fri Nov 15 15:31:13 2024 +0100

    Ensure ch_transcript_lengths and ch_control_features being channels and not arrayLists

commit 95a9b25
Author: bjlang <>
Date:   Fri Nov 15 13:17:02 2024 +0100

    Forward version channel from subworkflows

commit 846ca55
Author: bjlang <>
Date:   Fri Nov 15 13:01:11 2024 +0100

    Fix tests; add version channels; remove params access in subworkflow

commit 440e40f
Author: bjlang <>
Date:   Wed Nov 13 16:29:32 2024 +0100

    fix linting

commit ad3173e
Author: bjlang <>
Date:   Wed Nov 13 14:07:30 2024 +0100

    Fix test runs to finish except for GSEA

commit 69f5b36
Merge: 4ade9e2 6d0d3b8
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Mon Nov 4 20:52:11 2024 +0100

    Merge branch 'dev-ratio' into 311-add-module-gsea

commit 6d0d3b8
Merge: 0f9c9fc 953eb51
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Nov 4 16:39:50 2024 +0100

    Merge pull request #318 from bjlang/dev-ratio

    move pathway related logic out of differential and correlation subworkflows

commit 0f9c9fc
Merge: 4889998 a885116
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Nov 4 11:16:02 2024 +0100

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

    322 add module deseq2

commit a885116
Author: Breeshey Roskams-Hieter <42788995+roskamsh@users.noreply.github.com>
Date:   Wed Oct 30 14:22:13 2024 +0000

    update channel name to samples_and_matrix

    Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com>

commit 0e4a84d
Author: Breeshey Roskams-Hieter <42788995+roskamsh@users.noreply.github.com>
Date:   Wed Oct 30 14:22:03 2024 +0000

    update channel name to samples_and_matrix

    Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com>

commit a282a47
Author: Breeshey Roskams-Hieter <42788995+roskamsh@users.noreply.github.com>
Date:   Wed Oct 30 14:21:45 2024 +0000

    update channel name to samples_and_matrix

    Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com>

commit a2ddd8a
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Wed Oct 30 11:34:53 2024 +0000

    fix linting

commit d6da7ad
Merge: ba1ea24 4889998
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Wed Oct 30 11:31:14 2024 +0000

    resolve merge conflicts

commit ba1ea24
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Wed Oct 30 11:23:57 2024 +0000

    set nsub to lower numebr given nature of test data

commit 3546cb0
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Wed Oct 30 11:23:41 2024 +0000

    add DESEQ2 block to this workflow

commit 4a5aa60
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Wed Oct 30 11:21:12 2024 +0000

    add deseq2 pathway name

commit 953eb51
Author: bjlang <>
Date:   Wed Oct 30 12:15:10 2024 +0100

    Implement review comments

commit 1198761
Merge: f7c5c77 4889998
Author: bjlang <>
Date:   Wed Oct 30 11:17:05 2024 +0100

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

commit 4889998
Merge: 1d5b909 90001a2
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 30 10:51:47 2024 +0100

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

    add GPROFILER2 module to ENRICHMENT subworkflow

commit f7c5c77
Author: bjlang <>
Date:   Tue Oct 29 18:35:24 2024 +0100

    Adapt Limma call

commit 90001a2
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Tue Oct 29 16:34:18 2024 +0000

    add new line at end of file

commit 47bb659
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Tue Oct 29 16:32:45 2024 +0000

    remove trailing whitespace

commit 067c592
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Tue Oct 29 16:21:20 2024 +0000

    run GPROFILER2 only when enr_method is specified in the ch_tools channel

commit 02a38bb
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Tue Oct 29 16:20:21 2024 +0000

    add new pathway_names to test gprofiler2

commit e5a5d15
Merge: 94d3c8e 1d5b909
Author: bjlang <>
Date:   Tue Oct 29 17:02:24 2024 +0100

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

commit 94d3c8e
Author: bjlang <>
Date:   Tue Oct 29 16:56:29 2024 +0100

    Once more reorganize the pathway logic

commit f2b6322
Author: Breeshey Roskams-Hieter <breesheyroskams-hieter@Breesheys-MacBook-Pro.local>
Date:   Tue Oct 29 15:36:12 2024 +0000

    add GPROFILER2 module to ENRICHMENT subworkflow

commit 4ade9e2
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 15:42:12 2024 +0100

    add todo

commit 5620b42
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 15:41:03 2024 +0100

    Update test_experimental.config

commit b2868ae
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 15:36:34 2024 +0100

    Update CHANGELOG.md

commit 1d5b909
Merge: 1f4e926 f97ba6b
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 13:02:31 2024 +0100

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

    [dev-ratio] add limma to test_experimental

commit f97ba6b
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 12:48:48 2024 +0100

    add todo

commit 3b398ac
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 12:47:23 2024 +0100

    change filter_difftable_limma input column names

commit c6db7ff
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 12:04:26 2024 +0100

    fix bug

commit 898af43
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 11:57:18 2024 +0100

    add filtering step for limma

commit 4477e1c
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 11:48:29 2024 +0100

    add limma to test_experimental

commit 1f4e926
Merge: 0329206 e8067ac
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 11:23:50 2024 +0100

    Merge pull request #328 from syyang93/limma_add

    Modify differential/main.nf to include limma

commit e8067ac
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 10:49:11 2024 +0100

    trim trailing

commit afd7522
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 10:43:57 2024 +0100

    modify limma input

commit aca5f24
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 29 10:41:38 2024 +0100

    modify limma input

commit b530ddf
Author: Thomas Tams <tamstamsthomas@gmail.com>
Date:   Tue Oct 29 08:35:39 2024 +0000

    add: gsea into enrichment

commit af86bb2
Author: Stephanie Yang <stephanie.yuxin.yang@gmail.com>
Date:   Mon Oct 28 16:36:26 2024 +0100

    Modify differential/main.nf to include limma

commit b093261
Author: Thomas Tams <tamstamsthomas@gmail.com>
Date:   Mon Oct 28 14:51:13 2024 +0000

    feat: added GSEA to ENRICHMENT subworkflow, feeding channels from differentialabundance down to enrichment subworkflow

commit 517015b
Author: Thomas Tams <tamstamsthomas@gmail.com>
Date:   Mon Oct 28 14:14:06 2024 +0000

    add: activation of gsea_run and supplying gene set file

commit 0329206
Merge: 3c8be72 e345168
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Oct 28 12:22:29 2024 +0100

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

    shorten test_experimental into the essential tests

commit e345168
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Oct 28 11:33:18 2024 +0100

    trim trailing

commit 14b625b
Merge: 094452b 3c8be72
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Oct 28 11:27:20 2024 +0100

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

commit 094452b
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Oct 28 11:25:12 2024 +0100

    shorten test_experimental into the essential tests

commit 3c8be72
Merge: a594ebf dab58e5
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Fri Oct 25 14:41:51 2024 +0200

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

    [dev-ratio] update propr container and propd.R

commit dab58e5
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Fri Oct 25 13:10:53 2024 +0200

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

commit 8db59cc
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Fri Oct 25 13:08:16 2024 +0200

    update toolsheet

commit bd7d5d4
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 24 14:14:14 2024 +0200

    fix bug with number_of_cutoffs in propd.R

commit 74c77bd
Merge: f4e8164 a594ebf
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Wed Oct 23 19:05:58 2024 +0200

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

commit f4e8164
Author: bjlang <>
Date:   Wed Oct 23 19:05:11 2024 +0200

    Move pathway related logic out of differential and correlation SWF

commit a594ebf
Merge: aa03e1a 4075a80
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Wed Oct 23 15:51:50 2024 +0200

    Merge pull request #308 from bjlang/dev-ratio

    Split ch_tools into subworkflow relevant subchannels

commit 4075a80
Author: bjlang <>
Date:   Wed Oct 23 14:32:45 2024 +0200

    fix typo

commit 062c5a3
Author: bjlang <>
Date:   Wed Oct 23 14:16:50 2024 +0200

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

commit 9d35597
Author: bjlang <>
Date:   Wed Oct 23 11:27:12 2024 +0200

    remove duplicate tools declaration

commit 1cbdb17
Author: bjlang <>
Date:   Tue Oct 22 19:25:17 2024 +0200

    Fix linting and include propd_grea in test

commit 41adc93
Author: bjlang <>
Date:   Tue Oct 22 18:22:52 2024 +0200

    Split toolsheet data into subworkflow dedicated channels

commit 0464932
Author: bjlang <>
Date:   Tue Oct 22 11:40:01 2024 +0200

    finish merge

commit 95e406a
Merge: a6c2b3d aa03e1a
Author: bjlang <>
Date:   Tue Oct 22 11:20:00 2024 +0200

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

commit aa03e1a
Merge: e977214 ab9587b
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 22 10:33:07 2024 +0200

    Merge pull request #302 from suzannejin/dev-ratio

    [dev-ratio] add default parameters for propd/propr/grea

commit ab9587b
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Fri Oct 18 15:55:09 2024 +0200

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

commit b566842
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Fri Oct 18 11:12:09 2024 +0200

    updated propr container

commit 9819e84
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 17 18:06:59 2024 +0200

    add parameter for propd_weighted_degree

commit d7ab1ca
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 17 17:07:05 2024 +0200

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

commit a077c03
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 16:38:05 2024 +0200

    properly set the resources limits for test_experimental.config

commit bd51d59
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 16:24:36 2024 +0200

    fix error related to .nf-core.yml

commit 59bd17c
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 15:56:32 2024 +0200

    minor changes

commit 576bb8c
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 15:44:59 2024 +0200

    remove temporal config

commit 66148af
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 15:43:09 2024 +0200

    set toolsheet schema

commit 36fcff4
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 15:20:38 2024 +0200

    updated fromSamplesheet to samplesheetToList

commit e8f159a
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 14:55:44 2024 +0200

    udpate schema for tools

commit 46f1d8e
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 16 14:46:01 2024 +0200

    added the params for experimental workflow

commit e977214
Merge: f8811e4 83699b7
Author: Jonathan Manning <jonathan.manning@seqera.io>
Date:   Mon Oct 14 11:16:26 2024 +0100

    Merge branch 'dev' into dev-ratio

commit f8811e4
Merge: 25ace61 5c44e3c
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 10 11:38:52 2024 +0200

    Merge pull request #296 from suzannejin/dev-ratio

    [dev-ratio] update R template for propr local modules

commit 5c44e3c
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 10 11:12:10 2024 +0200

    change test_experimental to remove propd_grea (no container yet)

commit 118b257
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 10 10:51:41 2024 +0200

    added updated local version of propr/grea module

commit 38a32b6
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 17:01:20 2024 +0200

    fix bug in enrichment.nf

commit 5b56162
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 16:58:01 2024 +0200

    modified enrichment subworkflow to fit new grea module

commit cf58a2b
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 16:55:47 2024 +0200

    add local propr/grea module

commit fed6d45
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 16:18:38 2024 +0200

    remove nf-core/propr/grea

commit bc9c86a
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 16:11:07 2024 +0200

    fix bug in propr.R

commit 1696e1c
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 16:04:18 2024 +0200

    added local module propr/propr

commit 879b8a7
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 14:39:29 2024 +0200

    also get ch_results_genewise from propd

commit c74c341
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 14:37:33 2024 +0200

    test_experimental also run propd_fdr

commit c5ddf64
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 12:30:15 2024 +0200

    add comment

commit 36868e1
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 12:29:12 2024 +0200

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

commit 1731b3d
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 12:20:41 2024 +0200

    add more tests to experimental

commit ed06869
Merge: c36e237 8c75e55
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 12:19:25 2024 +0200

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

commit c36e237
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 12:17:49 2024 +0200

    prettier modules.json

commit 8c75e55
Author: nf-core-bot <core@nf-co.re>
Date:   Tue Oct 8 10:16:08 2024 +0000

    [automated] Fix code linting

commit b7a2774
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 12:09:28 2024 +0200

    trim trailing spaces

commit 6885bfd
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 11:55:28 2024 +0200

    added comment to propd.R

commit ecfc184
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Tue Oct 8 11:31:37 2024 +0200

    remove old container comment

commit aac7085
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Mon Oct 7 19:23:38 2024 +0200

    added new version propd

commit 25ace61
Merge: 293b30e 283385a
Author: Suzanne Jin <suzanne.jin.yao@gmail.com>
Date:   Mon Oct 7 15:39:18 2024 +0200

    Merge pull request #293 from suzannejin/dev-ratio

    [dev-ratio] simplified toolsheet structure, and modified the subworkflows accordingly

commit 283385a
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Thu Oct 3 11:57:32 2024 +0200

    updated modules.config with the correct nomenclature for grea

commit 7bc6ee8
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 17:29:48 2024 +0200

    remove filtervar related modules and subworkflows.

commit fc95675
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 17:29:03 2024 +0200

    updated schema_tools.json

commit c9b9482
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 15:04:27 2024 +0200

    remove trailing spaces

commit 3160a09
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 14:14:14 2024 +0200

    formatting

commit f4c4d2f
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 12:54:48 2024 +0200

    updated toolsheet to the current experimental workflow status

commit 328aacd
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 12:45:01 2024 +0200

    removed the variable selection block between diff and corr blocks.

commit ca6fb97
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 12:26:59 2024 +0200

    formatting

commit a0ef41b
Author: suzannejin <suzanne.jin.yao@gmail.com>
Date:   Wed Oct 2 12:22:36 2024 +0200

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

commit a6c2b3d
Author: bjlang <>
Date:   Tue Oct 1 16:30:48 2024 +0200

    Store output of different pathways in different folders

commit 293b30e
Merge: b71b83e 4a41e66
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Fri Sep 20 18:52:25 2024 +0200

    Merge pull request #290 from bjlang/dev-ratio

    minor code restructuring

commit 4a41e66
Author: bjlang <>
Date:   Fri Sep 20 18:43:24 2024 +0200

    minor code restructuring

commit b71b83e
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Fri Sep 13 15:53:15 2024 +0200

    Delete conf/crg.config

commit 9421df1
Merge: 6e6a740 318706a
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Tue Sep 10 15:27:14 2024 +0200

    Merge pull request #285 from bjlang/dev-ratio

    Dev ratio

commit 318706a
Author: bjlang <>
Date:   Fri Sep 6 19:37:41 2024 +0200

    fix testing parameters

commit 9532cfb
Author: bjlang <>
Date:   Fri Sep 6 19:04:56 2024 +0200

    fix linting

commit 8fcc24c
Author: bjlang <>
Date:   Fri Sep 6 18:58:22 2024 +0200

    Add CoDA/experimental branch to CI tests

commit d133c6d
Merge: 3254d25 2fe78de
Author: bjlang <>
Date:   Tue Sep 3 19:05:16 2024 +0200

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

commit 3254d25
Author: bjlang <>
Date:   Tue Sep 3 19:04:47 2024 +0200

    small fix

commit 2fe78de
Merge: 04abe25 6e6a740
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Tue Sep 3 18:42:02 2024 +0200

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

commit 04abe25
Author: bjlang <>
Date:   Tue Sep 3 18:01:29 2024 +0200

    - use validated input for experimental workflow
    - use contrast file information for differential analysis with PropD

commit 6e6a740
Merge: 5e5c6e4 3a69aae
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Tue Aug 27 15:08:32 2024 +0200

    Merge pull request #283 from bjlang/dev-ratio

    Include CoDa workflow in main workflow

commit 3a69aae
Merge: b218940 718075b
Author: bjlang <>
Date:   Tue Aug 27 14:56:48 2024 +0200

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

commit b218940
Author: bjlang <>
Date:   Tue Aug 27 14:53:28 2024 +0200

    Do not put not not in the not wrong place!

commit 718075b
Merge: 05cfb3a 5e5c6e4
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Tue Aug 27 14:38:12 2024 +0200

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

commit 5e5c6e4
Merge: e3fde5b c44e6bc
Author: Björn Langer <61791748+bjlang@users.noreply.github.com>
Date:   Tue Aug 27 14:34:36 2024 +0200

    Merge pull request #284 from nf-core/dev

    Update dev-ratio with changes from dev branch

commit 05cfb3a
Author: bjlang <>
Date:   Tue Aug 27 13:38:03 2024 +0200

    Move main_coda logic into differentialabundance as experimental study type

commit 0a3927a
Author: bjlang <>
Date:   Tue Jul 30 12:01:02 2024 +0200

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

commit 5a3727b
Author: bjlang <>
Date:   Fri Jul 26 17:47:12 2024 +0200

    Skip copying matrix if not necessary to allow resuming pipeline execution

commit 20c6cc6
Author: bjlang <>
Date:   Fri Jul 26 16:26:13 2024 +0200

    Use recommended format for optional parameters

commit d45c4aa
Author: bjlang <>
Date:   Fri Jul 26 15:57:01 2024 +0200

    Allow caching for -resume

commit e3fde5b
Author: bjlang <>
Date:   Fri Jul 26 11:13:35 2024 +0200

    small fixes to allow main_coda.nf to run

commit bf70167
Merge: 4986420 fc123ec
Author: caraiz2001 <105276325+caraiz2001@users.noreply.github.com>
Date:   Thu Jul 18 17:05:02 2024 +0200

    Merge pull request #281 from caraiz2001/dev-ratio

    Coda workflow.
    Files that are unique to the coda workflow have been added to the corresponding folders (conf, modules, subworkflows...). Files that are present in the pipeline have been added as ***_coda to avoid overwriting the original ones (modules_coda.config, nextflow_coda.config, main_coda.nf... etc).

commit fc123ec
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 16:52:17 2024 +0200

    install propr/propr with nf-core modules install

commit 8b25351
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 16:47:30 2024 +0200

    fix pre-commit errors in .json files

commit d60f031
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 16:37:50 2024 +0200

    install propd with nf-core modules install

commit 45b776e
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 16:34:09 2024 +0200

    modify propr main.nf to match nf-core repository

commit b59f668
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 15:54:12 2024 +0200

    update propr/grea with nf-core modules install

commit a2d3824
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 15:47:56 2024 +0200

    solve remaining lint erros

commit 969d15a
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 15:45:39 2024 +0200

    fix linting errors

commit 6f8d5b0
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 15:28:43 2024 +0200

    upload mygene module with nf-core module install

commit a91626b
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 15:00:33 2024 +0200

    add YMC counts and samplesheet to help for testing

commit 7487789
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 14:43:34 2024 +0200

    add nextflow.config and nextflow schema as nextflow_coda and nextflow_schema_coda

commit da30859
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 14:35:32 2024 +0200

    add main.nf as main_coda.nf

commit 93ae92d
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 14:25:33 2024 +0200

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

commit 4a76cef
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 14:18:19 2024 +0200

    add schema_tools and tools_samplesheet to assets

commit 708c4db
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 10:53:14 2024 +0200

    add functional subworkflows into subworkflows/local

commit eff2e81
Author: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date:   Thu Jul 18 10:38:04 2024 +0200

    add propr, mygene and fiter_var module
@suzannejin
Revert squashed commit of dev-ratio to updated dev code.
4ae7888 
The purpose is to keep the contribution record, but the dev code clean.

This reverts commit a64d4d7.
@suzannejin
installed subworkflows and associated modules
b68f1e1
@suzannejin
update modules
e38ad36
@suzannejin
update workflow to use the updated modules. It runs through test prof…
9cbe267 
…ile, but still need to check nf-test
@suzannejin
[abundance_differential_filter] separate channels for rlog and vst
3ee143c
@suzannejin
[subworkflows] remove mergeMaps. Otherwise the contrastid_expid forma…
9bd6518 
…t of output file names lead to error at rmarkdown step.
@suzannejin
update modules.config
dc74b0f
@suzannejin
[workflow] a first version that calls the subworkflows and properly r…
5844aea 
…uns till the end. Still need to pass nf-test
@suzannejin
fix pre-commit
84484a2
@suzannejin
[module] revert gsea seed to its previous behaviour. This will pass t…
1830f1f 
…he default pipeline test
@suzannejin
update test.snap
7d3bfbe
@suzannejin
[workflow] set ch_gene_sets and ch_background to Channel.of([[]]) whe…
b4d5630 
…n not provided
@suzannejin
[pipeline] update modules.config to add LIMMA_NORM config, when using…
83ebd1f 
… limma voom for rnaseq.
@suzannejin
update test_rnaseq_limma snapshot
62ad126
@suzannejin
merge from dev - after new yaml contrast logic is introduced
5fd7781
@suzannejin
[bug] update workflow to properly handle ch_norm
fac8a3d
@suzannejin
update test snapshots
a90148d
@suzannejin
[test] update test snapshots - from singularity to docker
63bb650
@suzannejin
Merge pull request #430 from suzannejin/dev-ratio-new
692da91 
integrate subworkflows into pipeline
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d4baddb

+| ✅ 307 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-differentialabundance_logo_dark.png">\n <img alt="nf-core/differentialabundance" src="docs/images/nf-core-differentialabundance_logo_light.png">\n \n

    \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/differentialabundance is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline \n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/differentialabundance \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/differentialabundance was originally written by Oskar Wacker, Jonathan Manning.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #differentialabundance channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/differentialabundance for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-02-21 13:19:07

@suzannejin
[modules] revert deseq2 modules into the version originally installed…
b96540f 
… in the pipeline - to avoid test snapshots inconsistencies related to decimal handling
@suzannejin
[feature] update differential subworkflow and pipeline for a common v…
de82c13 
…ariance_stabilised_matrix channel. Also fixed the code in the pipeline to properly handle it
@suzannejin
update changelog
4f039eb
This was referenced Jan 31, 2025
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Hello! @pinin4fjords
Here I added the nf-core subworkflows, and replaced the calls to the modules by calls to the subworkflows. Let me know what you think :)

NOTE that I had to make some small modifications in the subworkflows, please check them in nf-core/modules#7414.

I unabled the seed option discussed in #420 just temporarily,
I think it will be fine since you will change it anyway after implementing the global seed option @grst @nschcolnicov

cc @mirpedrol, @JoseEspinosa

@suzannejin suzannejin marked this pull request as ready for review January 31, 2025 16:25
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Hello! @pinin4fjords Here I added the nf-core subworkflows, and replaced the calls to the modules by calls to the subworkflows. Let me know what you think :)

NOTE that I had to make some small modifications in the subworkflows, please check them in nf-core/modules#7414.

I unabled the seed option discussed in #420 just temporarily, I think it will be fine since you will change it anyway after implementing the global seed option @grst @nschcolnicov

cc @mirpedrol, @JoseEspinosa

Thanks @suzannejin ! I want to be really careful with this one, and I'm travelling for work a lot this week, so bear with me as I review.

Made a couple of comments on the other one

pinin4fjords
pinin4fjords requested changes Feb 19, 2025
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Thanks for the simplifications, I think that's looking easier to parse. Still a couple of clarifications I'd like.

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75ae63f 
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
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@nf-core-bot lint

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@nf-core-bot fix-linting

suzannejin and others added 3 commits February 19, 2025 17:24
@pinin4fjords pinin4fjords requested a review from grst February 19, 2025 17:46
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Thanks for working with me on the simplifications @suzannejin , I think it's looking cleaner now.

I'm reasonably happy now and I'll approve so things aren't blocked (I'm just going on leave for a couple of days).

Given the major shift this represents, I'd be happier if a 3rd pair of eyes could look it over (maybe @grst ?). Could you try to make that happen before you merge?

pinin4fjords
pinin4fjords approved these changes Feb 19, 2025
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Approving to stop myself being a blocker, I'd be happier if we had a further review before merge.

nschcolnicov
nschcolnicov approved these changes Feb 20, 2025
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LGTM

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@pinin4fjords @suzannejin I'd really appreciate it if this PR could be merged once the conflicts are resolved, as it's currently blocking the development of other features. In any case, we can always open new PRs to address any follow-up issues.

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@nschcolnicov i agree with you on that, i am merging it today

@suzannejin suzannejin merged commit 801ecad into dev Feb 21, 2025
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@suzannejin suzannejin mentioned this pull request Feb 21, 2025
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@suzannejin suzannejin linked an issue Feb 21, 2025 that may be closed by this pull request
Integrate subworkflows into pipeline #383
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@nschcolnicov nschcolnicov nschcolnicov approved these changes

@grst grst Awaiting requested review from grst

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Integrate subworkflows into pipeline
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@suzannejin @nf-core-bot @pinin4fjords @nschcolnicov