Release 2.3.0 #230

jonasscheid · 2024-02-14T10:02:15Z

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).

…s-2-9 Merging template updates 2 9

…variant input

Co-authored-by: Jonas Scheid <[email protected]>

Check sample sheet uses Row Checker class

updating README + show_supported_models fix

Clean up CI tests

christopher-mohr · 2024-02-17T07:55:50Z

I just removed the "old" CI tests from the required checks

christopher-mohr

A couple of suggestions so far, I will continue later.

.nf-core.yml

assets/schema_input.json

docs/usage.md

lib/WorkflowEpitopeprediction.groovy

modules/local/epytope_peptide_prediction.nf

modules/nf-core/fastqc/environment.yml

christopher-mohr

Some additional comments/suggestions

bin/check_requested_models.py

CHANGELOG.md

Prepare release

mapo9

looks very nice!
Only some minor stuff

docs/usage.md

nextflow.config

nextflow_schema.json

…ture

Merge template 2.13.

christopher-mohr · 2024-02-23T10:20:53Z

Let's get another review for this once tests pass because of the most recent template change.

mapo9

LGTM! 🚀

just one minor change to improve readability of a parameter

nextflow_schema.json

christopher-mohr

LGTM

sync dev

…mart archives

Remove duplication in README and genome reference enum

nf-core-bot and others added 30 commits April 28, 2023 14:21

Template update for nf-core/tools version 2.8

c5b85c9

Template update for nf-core/tools version 2.9

8d10e90

Merge branch 'TEMPLATE' of https://github.com/nf-core/epitopeprediction

818f3f2

Add missing params to schema

cfe534d

add when condition

60a3de3

update nf-core modules

18e5c91

set version to dev

0658273

fix mqc config yml

0315d16

remove conda.enabled default

4bcaaee

remove remaining TODOs

91c2572

add PR number to CHANGELOG

6673444

readd conda.enabled default

90d1317

remove fastqc from pipeline tools

5402fd3

Update affiliation

439c317

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

Update CHANGELOG.md

c74333b

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

Fixing valid sample sheet printing

776668e

Change nomenclature of file_type

e1eeebd

Black formatting

18507f6

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 and others added 4 commits February 16, 2024 08:00

Merge remote-tracking branch 'origin/dev' into show_supported_models_fix

8e4c198

Merge pull request #225 from nf-core/show_supported_models_fix

b6d9cf4

updating README + show_supported_models fix

clean up CI tests

1033fc8

Merge pull request #231 from christopher-mohr/fix_ci_tests

14cafe5

Clean up CI tests

christopher-mohr reviewed Feb 17, 2024

View reviewed changes

christopher-mohr reviewed Feb 19, 2024

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bin/check_requested_models.py Outdated Show resolved Hide resolved

CHANGELOG.md Show resolved Hide resolved

jonasscheid and others added 3 commits February 19, 2024 23:59

Incorporate review

8691e1d

udpate changelog date

49f126a

Merge pull request #232 from jonasscheid/prepare-release

72e7e30

Prepare release

mapo9 requested changes Feb 20, 2024

View reviewed changes

nf-core-bot and others added 8 commits February 20, 2024 15:28

Template update for nf-core/tools version 2.13

6f8f3c6

merge template, fix conflicts, adjust for new local subworkflow struc…

d89ce8e

…ture

fix outdated param in grch38 test

4e232c7

incorporate release review requests

06702bb

fix readme

48eeb0f

fix ensembl default (grch38) url

90349c0

add newline to readme for proper display of hyperlinks

155b80f

Merge pull request #234 from jonasscheid/prepare-release

84252c5

Merge template 2.13.

jonasscheid requested a review from mapo9 February 23, 2024 12:06

mapo9 approved these changes Feb 23, 2024

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

christopher-mohr approved these changes Feb 23, 2024

View reviewed changes

jonasscheid and others added 6 commits February 25, 2024 20:58

Merge pull request #6 from jonasscheid/dev

ed86428

sync dev

remove duplicated warning from readme

40f846b

remove genome reference enum which might block specifying special bio…

504919e

…mart archives

bump release date

7e2f470

prettier readme

9e281b3

Merge pull request #235 from jonasscheid/prepare-release

1b82b50

Remove duplication in README and genome reference enum

jonasscheid merged commit e173620 into master Feb 26, 2024
37 checks passed

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Release 2.3.0 #230

Release 2.3.0 #230

jonasscheid commented Feb 14, 2024 •

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christopher-mohr commented Feb 17, 2024

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christopher-mohr commented Feb 23, 2024 •

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Release 2.3.0 #230

Release 2.3.0 #230

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jonasscheid commented Feb 14, 2024 • edited Loading

PR checklist

christopher-mohr commented Feb 17, 2024

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jonasscheid commented Feb 14, 2024 •

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christopher-mohr commented Feb 23, 2024 •

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