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Dev -> Master 2.5.0 #347

Merged
merged 49 commits into from
Oct 18, 2023
Merged

Dev -> Master 2.5.0 #347

merged 49 commits into from
Oct 18, 2023

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edmundmiller
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sateeshperi and others added 30 commits June 12, 2023 14:33
@sateeshperi
bump version 2.5.0dev
86d73c7
@sateeshperi
Merge pull request #326 from sateeshperi/dev
13cb0fe 
bump version 2.5.0dev
@nf-core-bot
Template update for nf-core/tools version 2.9
5ece807
@FelixKrueger
Update modules.config
9e2d80f 
Adding publish mode for coverage2cytosine NOMe-seq filtered GpC coverage files.
@FelixKrueger
Update CHANGELOG.md
107f736 
Added comment for coverage2cytosine publishing of files.
@ewels
Apply easy module updates
e048710 
Some other module updates are available, but those will require changes to the pipeline code.
@ewels
Changelog
ace1a39
@ewels
Merge pull request #331 from FelixKrueger/publish_coverage_files
e576ec8 
Publish coverage files
@edmundmiller
Merge branch 'dev' into nf-core-template-merge-2.9
6afd472
@edmundmiller
Merge pull request #329 from nf-core/nf-core-template-merge-2.9
b565c21 
Important! Template update for nf-core/tools v2.9
@edmundmiller
Merge branch 'dev' into master
b58eb2a
@edmundmiller
Merge pull request #333 from ewels/master
76ef5de 
Apply easy module updates
@wassimsalam01 @edmundmiller
Update nextflow_schema.json
2caf09e 
Updated zymo preset "--clip_r2" argument value from 15 to 10.
@wassimsalam01 @edmundmiller
Update nextflow_schema.json
591cc41 
Updated all em_seq preset argument values from 8 to 10.
@edmundmiller
Merge pull request #335 from update_kit_schema
16007cf 
Wrong display values for "zymo" and "em_seq" presets on help page
@edmundmiller
refactor: Use fromSamplesheet instead of input_check
7910cc1
@edmundmiller
fix: Add some magic from rnaseq
47d631c
@edmundmiller
chore: Update CHANGELOG
b6bb69f
@edmundmiller
chore: Update snapshots
675f73c
@sateeshperi
update tests, snapshots and ci
0cd09ec
@edmundmiller
Merge pull request #341 from nf-core/fromSamplesheet
89b0aa4 
Use fromSamplesheet
@maxulysse
Update nextflow.config
1737eda 
support pipeline-specific configs
@sateeshperi
Merge pull request #343 from nf-core/maxulysse-patch-1
c5bbf8e 
Support pipeline-specific configs
@nf-core-bot
Template update for nf-core/tools version 2.10
8e2a6f3
@edmundmiller
docs: Update Maintainers
ee70918
@edmundmiller
chore: Add CODEOWNERS file
766a26b
@edmundmiller
chore: Update CHANGELOG
92312de
@edmundmiller
Merge pull request #345 from nf-core/maintainers
0fe9fbd 
Maintainers
@edmundmiller
Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…
4ae729b 
…-2.10
@edmundmiller
Merge pull request #344 from nf-core/nf-core-template-merge-2.10
8e1411a 
Important! Template update for nf-core/tools v2.10
@edmundmiller edmundmiller added this to the 2.5.0 milestone Oct 18, 2023
@edmundmiller edmundmiller self-assigned this Oct 18, 2023
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github-actions bot commented Oct 18, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e02fd8c

+| ✅ 153 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-18 10:03:07

@edmundmiller edmundmiller marked this pull request as draft October 18, 2023 08:35
@edmundmiller edmundmiller requested review from a team and FelixKrueger October 18, 2023 08:54
sateeshperi and others added 4 commits October 18, 2023 09:10
@sateeshperi
add emojis to changelog v2.5.0
45c4468
@sateeshperi
bump snapshots for 2.5.0 release
1814838
@edmundmiller @sateeshperi
style: Ignore MultiQC config
f4fe5fd 
I refuse to update this every release.

Co-authored-by: sateeshperi <sateeshperi@users.noreply.github.com>
@edmundmiller
Merge pull request #348 from nf-core/release-prep
e02fd8c 
Release Prep for 2.5.0
@edmundmiller edmundmiller marked this pull request as ready for review October 18, 2023 09:45
FelixKrueger
FelixKrueger approved these changes Oct 18, 2023
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LGTS. Very nice work!

sateeshperi
sateeshperi approved these changes Oct 18, 2023
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LGTF&S

let's go

@edmundmiller edmundmiller merged commit 053e59e into master Oct 18, 2023
10 of 11 checks passed
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@FelixKrueger FelixKrueger FelixKrueger approved these changes

@sateeshperi sateeshperi sateeshperi approved these changes

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Hackathon: November 2023
Status: Done
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Status: Done
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2.5.0
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@edmundmiller @FelixKrueger @sateeshperi @nf-core-bot @ewels @wassimsalam01 @maxulysse