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First official release#17

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OlivierCoen wants to merge 504 commits intomasterfrom
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First official release#17
OlivierCoen wants to merge 504 commits intomasterfrom
dev

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@OlivierCoen
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@OlivierCoen OlivierCoen commented Mar 19, 2026

This PR is dedicated to officially releasing the pipeline in version 1.0.0.

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!
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@OlivierCoen
mapping gene ids against geo platform taxon instead of species
a163678
@OlivierCoen
add failures and warnings of normalisation and dataset cleaning to mu…
6460cae 
…ltiqc
@OlivierCoen
update .gitignore to ignore galaxy test files
a396d4e
@OlivierCoen
fix discrepancies following git am
83a3ae7
@OlivierCoen
Template update for nf-core/tools version 3.3.2
4659d78
@OlivierCoen
Merge branch 'TEMPLATE' into dev
ee84f92
@OlivierCoen
fix various issues linked to merge
77db12c
@OlivierCoen
fix output issue with expression atlas get accessions
0fe67d1
@OlivierCoen
early fix of release_annoucements.yml
ab7922a
@OlivierCoen
fix malformed nextflow schema
134bb45
@OlivierCoen
pass all module tests
6445bfd
@OlivierCoen
remove tag "module" in module tests
f5d82d1
@OlivierCoen
add missing module tests
e02ca8d
@OlivierCoen
allow tsv file as input dataset; modify id mapping script to allow that
80f543f
@OlivierCoen
allow tsv files in normalisation (deseq2 and edger)
91b9155
@OlivierCoen
update documentation
64bcdf8
@OlivierCoen
change species parameter to allow more complex species names; add spe…
433dfea 
…cies tag in get accessions modules; display a warn message when no dataset is found
@OlivierCoen
update README.md
c9b9dd4
@OlivierCoen
fix .github/workflows/release-announcements.yml with latest code
7ddbf89
@OlivierCoen
update get_geo_dataset_accessions.py to improve output and allow rnas…
7bfb57c 
…eq data
@OlivierCoen
clean code; remove superseries from geo accessions
efbaad3
@OlivierCoen
allow geo datasets containing multiple datasets
3b09364
@OlivierCoen
change base.config times
c6bbfad
@OlivierCoen
add troubleshooting doc
3821964
@OlivierCoen
pass pipeline nf-tests
90d5b87
@OlivierCoen
allow and improve downloading of RNAseq data from GEO
2c07114
@OlivierCoen
force integer count values after mapping to ensembl gene IDs
660214c
@OlivierCoen
functional download and parsing of rnaseq data from GEO
404f85a
@OlivierCoen
set ks threshold pvalue as negative by default
5aa1acc
@OlivierCoen
fix issue with deseq2 and edger in case of only one sample; improve l…
459d726 
…ogging
OlivierCoen and others added 30 commits March 22, 2026 13:48
@OlivierCoen
better handle connection issues in expression atlas getdata
f3c557d
@OlivierCoen
update broken links in documentation
89fdc04
@OlivierCoen
update snapshots
1564c47
@OlivierCoen
update min version of Nextflow
acbc1b1
@OlivierCoen
add contributors
68898d7
@OlivierCoen
update min Nextflow version to 25.10.4
32d543d
@OlivierCoen
act possibility to run nf-test through act
18d41b8
@OlivierCoen
add pipeline test command to README.md
35a1081
@OlivierCoen
Update default.nf.test.snap
960571d
@OlivierCoen
add act tests
5cfd8bc
@OlivierCoen
fix tests
b989a35
@OlivierCoen
authorize failure and ignore error for expression get data and geo de…
95dd20e 
…t data
@OlivierCoen
fix tests
d94cb49
@OlivierCoen
improve testing with act and add README.md
7f81d56
@OlivierCoen
update checkCounts function
68627a8
@OlivierCoen
fix weird insertions in snapshots
237ec2c
@OlivierCoen
add skewness.csv to .nftignore
b79fde2
@OlivierCoen
update snapshots
12d33f8
@OlivierCoen
fix reproductibility issue
f7c4a50
@OlivierCoen
fix skewness issue
abcda5e
@OlivierCoen
fix issue with act
d876bbd
@OlivierCoen
remove a pipeline test
25e7791
@OlivierCoen
Update nf-test.yml
5919420
@OlivierCoen
update snapshots
772ca82
@OlivierCoen
fix prettier error
3a3c759
@OlivierCoen
update multiqc
a946490
@OlivierCoen
adapt pipeline to new multiqc input syntax
21489b2
@OlivierCoen
remove tests involving geo get data
d315b9e
@OlivierCoen
improve testing with act
0f2b6af
@Ositofeliz
Merge pull request #18 from OlivierCoen/dev
734cf2e 
Fix some bugs and pass tests with conda and apptainer
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3 participants

@OlivierCoen @nf-core-bot @Ositofeliz