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Release 2.3.0 #230

Merged
merged 126 commits into from
Feb 26, 2024
Merged

Release 2.3.0 #230

merged 126 commits into from
Feb 26, 2024

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jonasscheid
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@jonasscheid jonasscheid commented Feb 14, 2024 •
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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/epitopeprediction branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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).

nf-core-bot and others added 30 commits April 28, 2023 14:21
@nf-core-bot
Template update for nf-core/tools version 2.8
c5b85c9
@nf-core-bot
Template update for nf-core/tools version 2.9
8d10e90
@christopher-mohr
Merge branch 'TEMPLATE' of https://github.com/nf-core/epitopeprediction
818f3f2
@christopher-mohr
Add missing params to schema
cfe534d
@christopher-mohr
add when condition
60a3de3
@christopher-mohr
update nf-core modules
18e5c91
@christopher-mohr
set version to dev
0658273
@christopher-mohr
fix mqc config yml
0315d16
@christopher-mohr
remove conda.enabled default
4bcaaee
@christopher-mohr
remove remaining TODOs
91c2572
@christopher-mohr
add PR number to CHANGELOG
6673444
@christopher-mohr
readd conda.enabled default
90d1317
@christopher-mohr
remove fastqc from pipeline tools
5402fd3
@christopher-mohr
Update affiliation
439c317
@christopher-mohr
Merge pull request #203 from christopher-mohr/merging-template-update…
13ce412 
…s-2-9

Merging template updates 2 9
Restructure input check and samplesheet check
54ea01e
Add MIT license for check_samplesheet.py
9e1513b
Add information to CHANGELOG.md and fix bug in check_samplesheet for …
4110373 
…variant input
Black formatting
b974bd3
@alina-bauer
Update CHANGELOG.md
c74333b
@alina-bauer @jonasscheid
Add suggestions from PR to code
a645848 
Co-authored-by: Jonas Scheid <[email protected]>
Fix output printing and keep name inputtype for nomenclature of meta
4ec0102
Remove test code
01d1fea
@alina-bauer
Fixing valid sample sheet printing
776668e
@alina-bauer
Change nomenclature of file_type
e1eeebd
Black formatting
18507f6
@jonasscheid
Merge pull request #209 from alina-bauer/mhc-binding-subworkflow
50812f9 
Check sample sheet uses Row Checker class
Add option to enter alleles as internet link to samplesheet
e6e441e
Fix nomenclature of inputtype in check_samplesheet file
71e843b
Now possible to add allele txt file in local folder
89259c6
@christopher-mohr
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I just removed the "old" CI tests from the required checks

christopher-mohr
christopher-mohr reviewed Feb 17, 2024
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A couple of suggestions so far, I will continue later.

.nf-core.yml Outdated Show resolved Hide resolved
assets/schema_input.json Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
lib/WorkflowEpitopeprediction.groovy Outdated Show resolved Hide resolved
lib/WorkflowEpitopeprediction.groovy Outdated Show resolved Hide resolved
modules/local/epytope_peptide_prediction.nf Show resolved Hide resolved
modules/nf-core/fastqc/environment.yml Outdated Show resolved Hide resolved
christopher-mohr
christopher-mohr reviewed Feb 19, 2024
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Some additional comments/suggestions

bin/check_requested_models.py Outdated Show resolved Hide resolved
bin/check_requested_models.py Outdated Show resolved Hide resolved
CHANGELOG.md Show resolved Hide resolved
mapo9
mapo9 requested changes Feb 20, 2024
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looks very nice!
Only some minor stuff

docs/usage.md Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
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christopher-mohr commented Feb 23, 2024 •
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Let's get another review for this once tests pass because of the most recent template change.

mapo9
mapo9 approved these changes Feb 23, 2024
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LGTM! 🚀

just one minor change to improve readability of a parameter

nextflow_schema.json Outdated Show resolved Hide resolved
christopher-mohr
christopher-mohr approved these changes Feb 23, 2024
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LGTM

@jonasscheid jonasscheid merged commit e173620 into master Feb 26, 2024
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@christopher-mohr christopher-mohr christopher-mohr approved these changes

@mapo9 mapo9 mapo9 approved these changes

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@jonasscheid @christopher-mohr @mapo9 @nf-core-bot @alina-bauer