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Release 1.5.0 #256

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merged 226 commits into from
May 8, 2024
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8f537bf
Added round param for all modules (currently active for proteus und g…
WackerO Oct 31, 2023
5c203cc
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Oct 31, 2023
1b891c5
Param rename, reordered Citations, changed gprofiler2 report heading,…
WackerO Nov 7, 2023
dbb7355
Added docs entry for gprofiler
WackerO Nov 7, 2023
a0797b7
Corrected some entries in the schema
WackerO Nov 8, 2023
0af6ce1
integrated module changes
WackerO Nov 13, 2023
8ae788f
Added PI and contact params for report; added newline between report …
WackerO Nov 14, 2023
f7e2f7e
Newly installed gprofiler2 module, enabled it in full test
WackerO Nov 16, 2023
454c23c
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Nov 16, 2023
c7b93fc
added gprofiler to git
WackerO Nov 16, 2023
ac07d6e
prettier
WackerO Nov 16, 2023
52a5d08
Added gpro to test.config
WackerO Nov 16, 2023
d72f277
changing the workflow to make gprofiler run multiple times if several…
WackerO Nov 17, 2023
c289494
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Nov 21, 2023
a0f7ab1
GOST module update
WackerO Nov 23, 2023
786ec25
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Nov 27, 2023
f1205c5
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Nov 27, 2023
0df5a89
Removed write statements, updated metro map
WackerO Nov 27, 2023
68695b7
Corrected metro maps, uncommented error case in workflow, fixed spell…
WackerO Nov 27, 2023
5b7441b
bump versions
pinin4fjords Nov 27, 2023
c0c4de6
Fix resource issues
pinin4fjords Nov 27, 2023
c993eac
update changelog
pinin4fjords Nov 27, 2023
2b2caae
[automated] Fix linting with Prettier
nf-core-bot Nov 27, 2023
3f56135
Update changelog
pinin4fjords Nov 27, 2023
804d6e5
Merge branch 'de_resources' of github.com:nf-core/differentialabundan…
pinin4fjords Nov 27, 2023
f09a2fc
Merge pull request #208 from nf-core/de_resources
pinin4fjords Nov 27, 2023
0a24c7c
Added filtered DE tables to output; add rounding after gprofiler2 PR …
WackerO Nov 29, 2023
ffbae15
Renamed round_digits to report_round_digits, excluded gsea from defau…
WackerO Nov 30, 2023
57f83b8
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Nov 30, 2023
ced9196
fixed schema, added icons to proteus and gprofiler2
WackerO Nov 30, 2023
397192b
Update affy/justrma to pull in timeout fix
pinin4fjords Dec 1, 2023
2508403
Update changelog
pinin4fjords Dec 1, 2023
ccb10cf
Poke CI
pinin4fjords Dec 1, 2023
cf71f42
update changelog
pinin4fjords Dec 4, 2023
b7c822a
Merge pull request #210 from nf-core/include_affy_fix
pinin4fjords Dec 4, 2023
c80cec0
Fix volcano plot legend
pinin4fjords Dec 4, 2023
e4bfbf9
Update CHANGELOG
pinin4fjords Dec 5, 2023
b789237
Merge pull request #213 from nf-core/fix_volcano_legend
pinin4fjords Dec 5, 2023
04c9084
Combined gprofiler with gsea section in report results; added short g…
WackerO Dec 5, 2023
1685196
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Dec 5, 2023
ddeed39
Changed param name in two configs
WackerO Dec 5, 2023
5250c22
Fixed some old params
WackerO Dec 5, 2023
8519c11
added difftable filtering module, added short docu section for gsea, …
WackerO Dec 8, 2023
a1fcc1c
Param renames, adapted workflow to do the correct checks; fixed a bug…
WackerO Dec 8, 2023
a9a3558
Added gprofiler organism, updated metro maps
WackerO Dec 8, 2023
0fc06ec
Uploaded slimmer SVG, fixed mistake in ifelse
WackerO Dec 8, 2023
f08dae5
Updated gprofiler
WackerO Dec 8, 2023
24e7497
Reordered report param
WackerO Dec 8, 2023
806580c
removed empty line
WackerO Dec 8, 2023
c7c55ca
adapted gprofiler2 report section to gsea, changed order of docu, add…
WackerO Dec 13, 2023
513e00b
Removed prints
WackerO Dec 13, 2023
ab68a1c
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Dec 13, 2023
4989dc7
Renamed gene_sets param, updated gprofiler
WackerO Dec 13, 2023
afe5f5f
Added final newline
WackerO Dec 13, 2023
f971092
Removed redundant code lines
WackerO Dec 14, 2023
299d5ab
Update modules/local/filter_difftable.nf
WackerO Dec 14, 2023
7d5d6a0
Merge branch 'add_gpro' of https://github.com/WackerO/differentialabu…
WackerO Dec 14, 2023
57bb2c5
Fixed filter module, added gprofiler background docu
WackerO Dec 14, 2023
8bae50e
Removed token from full test
WackerO Dec 14, 2023
76a628a
Updated gprofiler docu
WackerO Dec 14, 2023
f026a95
Updated output docs
WackerO Dec 15, 2023
05e98ba
Added param for selectively running gprofiler2 without GMT
WackerO Dec 18, 2023
a89bc93
Streamline gene set conditionals, don't overwrite global gene sets ch…
pinin4fjords Dec 18, 2023
b2af649
removed gprofiler mode
WackerO Dec 19, 2023
5601543
Merge branch 'add_gpro' of https://github.com/WackerO/differentialabu…
WackerO Dec 19, 2023
cd3bdf5
Template update for nf-core/tools version 2.11
nf-core-bot Dec 19, 2023
e1cc292
Update workflows/differentialabundance.nf
WackerO Dec 20, 2023
fe404cc
Update docs/usage.md
WackerO Dec 20, 2023
d4b6370
Added .first() to gene sets for gprofiler, made error message more sp…
WackerO Dec 20, 2023
2273996
prettier
WackerO Dec 20, 2023
4ec05c1
lint
WackerO Dec 20, 2023
18f5f44
Linting
WackerO Dec 20, 2023
68d203f
prettier
WackerO Dec 20, 2023
f1d407f
Template update for nf-core/tools version 2.11.1
nf-core-bot Dec 20, 2023
cc429e7
Merge pull request #199 from WackerO/add_gpro
WackerO Dec 21, 2023
418bd04
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Dec 21, 2023
4b12f71
Merge branch 'nf-core-template-merge-2.11.1' of https://github.com/nf…
WackerO Dec 21, 2023
82c96b0
Undid some unnecessary changes
WackerO Dec 21, 2023
3a12411
reinstalled matrixfilter to fix linting
WackerO Dec 21, 2023
f0f0411
Update assets/multiqc_config.yml
pinin4fjords Dec 21, 2023
86b933b
prettier
WackerO Dec 21, 2023
da334d7
Updated changelog
WackerO Dec 21, 2023
cbcda65
Merge pull request #219 from nf-core/nf-core-template-merge-2.11.1
WackerO Dec 21, 2023
a254961
Update shinyngs modules to address density plots issue
pinin4fjords Jan 8, 2024
cc159c2
update CHANGELOG
pinin4fjords Jan 8, 2024
1350e4b
Added rounds to numeric tables
WackerO Jan 9, 2024
8baf8f4
Removed newline to rerun git tests
WackerO Jan 9, 2024
56944c7
Bump module to correct GSEA CLS file creation
pinin4fjords Jan 10, 2024
ba4e770
Update CHANGELOG
pinin4fjords Jan 10, 2024
8c8bb07
Update CHANGELOG.md
pinin4fjords Jan 10, 2024
d1730f8
Update CHANGELOG.md
pinin4fjords Jan 10, 2024
b21659c
Merge pull request #221 from nf-core/bump_shinyngs_for_density
pinin4fjords Jan 10, 2024
ba2b371
Merge branch 'dev' into tabulartogseacls_fieldcheck
pinin4fjords Jan 10, 2024
e2a132f
Merge pull request #223 from nf-core/tabulartogseacls_fieldcheck
pinin4fjords Jan 10, 2024
2e9560d
Update changelog
WackerO Jan 11, 2024
3ce6e97
Merge pull request #222 from WackerO/round_report
WackerO Jan 11, 2024
9d1d609
Changed report contact info to a single param and added CSS for styli…
WackerO Jan 16, 2024
745800b
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Jan 16, 2024
58b1394
Linting, bugfixes
WackerO Jan 16, 2024
5214258
Added gene_id_col to DESEQ2_NORM modules.config entry
WackerO Jan 18, 2024
4b1ff42
Changed contributor info from file to string param, simplified CSS an…
WackerO Jan 23, 2024
56415b0
Update changelog, prettier
WackerO Jan 23, 2024
ed5a486
Merge pull request #226 from WackerO/dev
WackerO Jan 23, 2024
3e9ef96
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Jan 23, 2024
bd23bec
Update changelog
WackerO Jan 23, 2024
b3f42c8
Renamed variable
WackerO Jan 24, 2024
d62c163
Update assets/differentialabundance_report.Rmd
WackerO Jan 27, 2024
6130058
Merge pull request #197 from WackerO/project_info
WackerO Jan 29, 2024
0a300ff
Template update for nf-core/tools version 2.12
nf-core-bot Jan 29, 2024
39d05e9
Merge branch 'dev' into nf-core-template-merge-2.12
WackerO Jan 30, 2024
0d234af
Fix linting
WackerO Jan 31, 2024
7b1b365
[automated] Fix linting with Prettier
nf-core-bot Jan 31, 2024
73bb532
Linting in report.Rmd
WackerO Jan 31, 2024
3d32706
Merge branch 'nf-core-template-merge-2.12' of https://github.com/nf-c…
WackerO Jan 31, 2024
95ad529
More linting, changelog update
WackerO Jan 31, 2024
b9ce2d6
Fix prettier issues
pinin4fjords Feb 2, 2024
3c21229
Merge pull request #228 from nf-core/nf-core-template-merge-2.12
pinin4fjords Feb 2, 2024
c28c101
GSEA update
WackerO Feb 8, 2024
ca4c967
Mention missing dots in volcano plot, change rounding, turn off round…
WackerO Feb 8, 2024
5421e4e
Merge pull request #231 from WackerO/dev
WackerO Feb 8, 2024
0d1832e
Changed 0 pval warning
WackerO Feb 12, 2024
3af76f2
Add note on scaling
pinin4fjords Feb 13, 2024
f08fcdb
extend scaling note
pinin4fjords Feb 13, 2024
e5f2ee3
Prettier
pinin4fjords Feb 13, 2024
b38d216
Also disable shinyngs at scale
pinin4fjords Feb 13, 2024
c22968c
Merge pull request #233 from nf-core/scaling_note
pinin4fjords Feb 13, 2024
ce772de
Template update for nf-core/tools version 2.13
nf-core-bot Feb 20, 2024
32a270b
Publish gsea reports
pinin4fjords Feb 21, 2024
60a0173
Update CHANGELOG.md
pinin4fjords Feb 21, 2024
99cdf5c
Reenabled default rounding
WackerO Feb 21, 2024
ebfd146
Merge branch 'TEMPLATE' of https://github.com/nf-core/differentialabu…
WackerO Feb 21, 2024
2e147be
trying to fix some issues after conflict solving
WackerO Feb 21, 2024
19e7574
Update nextflow_schema.json
WackerO Feb 22, 2024
00d42e0
Bugfixing
WackerO Feb 22, 2024
2e2bc74
Bugfixing; removed samplesheet definition from pipelineInitialization
WackerO Feb 23, 2024
337b741
Removed remaining custom_dumpsoftware references; removed prints and …
WackerO Feb 23, 2024
92f4cf7
Merge pull request #241 from WackerO/merging-template-updates
WackerO Feb 26, 2024
80a6dd4
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Feb 27, 2024
9a80df5
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Feb 27, 2024
e393cdd
Merge branch 'volcano_round' of https://github.com/WackerO/differenti…
WackerO Feb 27, 2024
e5d11f8
Merge pull request #232 from WackerO/volcano_round
WackerO Feb 27, 2024
d8ade86
Belatedly added NA options for matrixfilter to the pipeline
WackerO Feb 27, 2024
3843115
Corrected PR number
WackerO Feb 27, 2024
9af81ed
made proportion_not_na conditional
WackerO Feb 27, 2024
1e52820
Merge pull request #244 from WackerO/matrixfilter_na
WackerO Feb 28, 2024
e99fdc2
Template update for nf-core/tools version 2.13.1
nf-core-bot Feb 29, 2024
d27287d
Merge branch 'TEMPLATE' of https://github.com/nf-core/differentialabu…
WackerO Mar 13, 2024
51049b2
Changelog update
WackerO Mar 13, 2024
b7b8cea
Merge branch 'dev' into publish_gsea_reports
pinin4fjords Mar 13, 2024
77b72cc
Ran nf-core lint --fix files_unchanged
pinin4fjords Mar 13, 2024
5317df3
Fix logos
pinin4fjords Mar 13, 2024
da6dd3f
Fix logo
pinin4fjords Mar 13, 2024
feef653
Merge pull request #250 from WackerO/merging-template-updates
WackerO Mar 13, 2024
1f6adf5
Merge pull request #240 from nf-core/publish_gsea_reports
pinin4fjords Mar 13, 2024
adbc14f
Added QBiC credits, made observations_name_col optional on modules.co…
WackerO Mar 19, 2024
65550c5
Moved differential_file_suffix and exploratory_assay_names to advance…
WackerO Mar 20, 2024
5c08b3b
linting
WackerO Mar 20, 2024
13899f4
updated changelog
WackerO Mar 20, 2024
2d174ce
Version bump in preparation of release 1.5.0
WackerO Mar 20, 2024
37fa90a
Update README.md
WackerO Mar 21, 2024
a64c11a
Update conf/modules.config
WackerO Mar 21, 2024
0c352eb
Update conf/modules.config
WackerO Mar 21, 2024
ba94655
Update conf/modules.config
WackerO Mar 21, 2024
1f15666
Returned advanced options to their sections, removed default for obse…
WackerO Mar 21, 2024
8fa83dd
linting
WackerO Mar 21, 2024
82cba18
removed advanced options key from schema, re-added example of observa…
WackerO Mar 21, 2024
0854d3f
added description of observations_name_col default
WackerO Mar 22, 2024
2972621
Merge pull request #254 from WackerO/simplify
WackerO Mar 22, 2024
a899bb5
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Mar 22, 2024
de13cbf
Merge pull request #255 from WackerO/dev
WackerO Mar 25, 2024
76971c3
added maxquant profile to nextflow.config, clarified some docu, made …
WackerO Mar 27, 2024
d1f8d3b
prettier
WackerO Mar 27, 2024
5f25966
Trying to fix the pipeline pull issue
WackerO Mar 27, 2024
6520455
Bugfix in proteus_measurecol_prefix parameter with final whitespace
WackerO Mar 27, 2024
10e365e
prettier
WackerO Mar 27, 2024
a72c18b
Readded the projectDir to hopefully get rid of the download error
WackerO Mar 27, 2024
fbb214a
linting
WackerO Mar 27, 2024
c6a8353
more linting; fails locally despite same paths as in airrflow, but ma…
WackerO Mar 27, 2024
158cc1c
Added file params with defaults to linting ignore list as they are not
WackerO Mar 27, 2024
242cf96
checked out dev logos as the nf-core lint --fix files_unchanged comma…
WackerO Mar 27, 2024
088b0f9
prettier
WackerO Mar 27, 2024
b25f1fc
Update docs/usage.md
WackerO Apr 8, 2024
3d0f1c2
Update docs/usage.md
WackerO Apr 8, 2024
04ae35d
Update docs/usage.md
WackerO Apr 8, 2024
fb2681f
Bump gtf2featureannotation
pinin4fjords Apr 9, 2024
02a5656
update changelog
pinin4fjords Apr 9, 2024
6e158cb
Merge branch 'dev' into update_gtf2featureannotation
pinin4fjords Apr 9, 2024
314ee61
Merge pull request #259 from nf-core/update_gtf2featureannotation
pinin4fjords Apr 10, 2024
74d7acb
updated proteus module
WackerO Apr 12, 2024
c024383
Merge branch 'prerelease_fixes' of https://github.com/WackerO/differe…
WackerO Apr 12, 2024
cab1c01
Fixed filter_difftable module not properly filtering (had to switch t…
WackerO Apr 19, 2024
04eac80
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Apr 19, 2024
f1afb24
Updated changelog
WackerO Apr 19, 2024
dac77c9
linting
WackerO Apr 22, 2024
8750d89
moved log2 from workflow into filter module
WackerO Apr 22, 2024
d60b63b
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Apr 23, 2024
23a8270
changed filter_difftable to python
WackerO Apr 23, 2024
a9a7847
update changelog
WackerO Apr 23, 2024
456cb35
fixed PR number in changelog
WackerO Apr 23, 2024
b379fef
change nf-core.yml to fix linting
WackerO Apr 23, 2024
be656d9
removed writing python version
WackerO Apr 24, 2024
d6f50cb
fix typo
WackerO Apr 24, 2024
c2d7ed0
Merge pull request #264 from WackerO/fix_filter_difftable
WackerO Apr 24, 2024
d9fd29a
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Apr 24, 2024
fe03ce6
Merge pull request #257 from WackerO/prerelease_fixes
WackerO Apr 30, 2024
52cb0bb
GSEA- pngs and htmls in same place
pinin4fjords Apr 30, 2024
8562137
Update CHANGELOG.md
pinin4fjords Apr 30, 2024
ad437d1
log2 assays are not a features thing
pinin4fjords Apr 30, 2024
8de1934
All GSEA outputs in the same place
pinin4fjords Apr 30, 2024
7561759
Set logging in individual configs
pinin4fjords Apr 30, 2024
d86edbe
Update modules.config
pinin4fjords Apr 30, 2024
9f3ddd4
Update modules.config
pinin4fjords Apr 30, 2024
47306db
Merge pull request #265 from nf-core/gsea_html_fix
pinin4fjords Apr 30, 2024
3f423b5
Bump shinyngs
pinin4fjords May 2, 2024
6bcfd2b
Merge branch 'dev' into fix_logging
pinin4fjords May 2, 2024
5fe81f0
Bump shinyngs again
pinin4fjords May 3, 2024
1b3cbc8
Merge branch 'fix_logging' of github.com:nf-core/differentialabundanc…
pinin4fjords May 3, 2024
717d641
Update sw to fix linting
pinin4fjords May 3, 2024
4be285a
Add prettify fix to notebook
pinin4fjords May 3, 2024
b807bc8
Commit nf-test dirs from module updates
pinin4fjords May 3, 2024
7f6be6d
Update CHANGELOG
pinin4fjords May 7, 2024
9c1a6cf
Fix module install sources
pinin4fjords May 7, 2024
361fb75
Merge pull request #266 from nf-core/fix_logging
pinin4fjords May 7, 2024
fb37024
minor fixes for release, update changelog
WackerO May 8, 2024
3ec9d1e
fixed brackets in changelog
WackerO May 8, 2024
1c4158e
Merge pull request #267 from WackerO/dev
WackerO May 8, 2024
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Update conf/modules.config
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
WackerO and pinin4fjords authored Mar 21, 2024
commit 0c352ebe682f23252600bc4aa2f6e6b9ba183267
2 changes: 1 addition & 1 deletion conf/modules.config
Original file line number Diff line number Diff line change
@@ -85,7 +85,7 @@ process {
]
ext.prefix = { "normalised." }
ext.args = { [
((params.observations_name_col == null) ? "--sample_name_col \"${params.observations_id_col}\"" : "--sample_name_col \"${params.observations_name_col}\""),
"--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"",
"--file_name_col \"${params.affy_file_name_col}\"",
"--background ${params.affy_background}",
"--normalize True",