Dev -> main for 3.3.2 #3664

mashehu · 2025-07-08T08:06:43Z

PR checklist

This comment contains a description of changes (with reason)
CHANGELOG.md is updated
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

By default, we dissallow spaces in directory paths, which is an unnecessary limitation.

Update nf-core modules info command after meta.yml restructuring

…xtflow config --flat

… backtracking and assign them to the dict as well.

…ers parsed from main.nf

The current parser that converts the output of `nextflow config --flat` into a Python dict fails to capture multi-line config values correctly, because it used `.splitlines()`. I have replaced this logic with one that is hopefully able to capture those as well without breaking existing code.

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

codecov · 2025-07-08T08:16:22Z

Codecov Report

Attention: Patch coverage is 87.52643% with 59 lines in your changes missing coverage. Please review.

Project coverage is 77.08%. Comparing base (5e54606) to head (e1cc6c9).
Report is 167 commits behind head on main.

Files with missing lines	Patch %	Lines
nf_core/modules/lint/__init__.py	37.50%	45 Missing ⚠️
nf_core/test_datasets/test_datasets_utils.py	86.36%	3 Missing ⚠️
nf_core/modules/lint/meta_yml.py	93.10%	2 Missing ⚠️
nf_core/pipelines/create_logo.py	71.42%	2 Missing ⚠️
nf_core/pipelines/lint/nf_test_content.py	94.73%	2 Missing ⚠️
nf_core/components/info.py	93.75%	1 Missing ⚠️
nf_core/pipelines/create/__init__.py	0.00%	1 Missing ⚠️
nf_core/pipelines/create/custompipeline.py	90.90%	1 Missing ⚠️
nf_core/pipelines/create/utils.py	87.50%	1 Missing ⚠️
nf_core/pipelines/lint_utils.py	87.50%	1 Missing ⚠️

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* Update python:3.13-slim Docker digest to 6544e0e * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Fix wrong key when updating module outputs

Co-authored-by: nf-core-bot <core@nf-co.re>

CHANGELOG.md

jfy133 and others added 30 commits January 17, 2025 08:57

Remove unused stub args variable to satisfy langauge server

9218227

[automated] Update CHANGELOG.md

b6aebbd

Merge branch 'dev' into remove-args-stub

a5ebded

Update CHANGELOG.md

06613cb

generate modules meta.yml with python

e8b4881

[automated] Update CHANGELOG.md

19def72

add ontology term to versions.yml

a048156

add pytests for all possible module templates

0d9abe3

fix test mocks

bf7b59f

generaet meta.yml only for modules

34b1499

bump nf-schema to 2.4.0

6ec32ed

add PR number to changelog

3c21928

remove tmp files

a628c8e

fix lint tests

3cb6cb0

update ci nextflow version of tools

aaa4359

fix version typo

88c29ff

Update CHANGELOG.md

63a31c4

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

Update nf_core/pipeline-template/nextflow.config

4e31eb4

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

update linting with correct meta.yml structure

b4cc700

update to python 3.9, support 3.13

3f0e2a0

run ruff upgrader to 3.9

a84ad0b

[automated] Update CHANGELOG.md

1e71a92

Merge branch 'dev' into add-py-3_13

52d3df5

Merge branch 'dev' into meta-yml-tuple-structure

85991d3

fix mypy notation for python 3.8

24ce188

By default, provide a more flexible fastq pattern

01c091d

By default, we dissallow spaces in directory paths, which is an unnecessary limitation.

Update nf_core/components/nfcore_component.py

273bc79

Merge branch 'dev' into add-py-3_13

b50deec

run ruff autofixer

e0e83e0

fix modules path

f4f260d

mirpedrol and others added 18 commits July 7, 2025 14:16

fix tests after meta.yml restructuring

fb24202

[automated] Update CHANGELOG.md

cf68dea

update pipeline template modules

a1a732a

update pipeline nf-test snapshots

dd3dc6d

multiqc parquet file is not stable

9ae0239

update fastqc and default snapshots

6f3b319

Update CHANGELOG.md

a490554

Merge pull request #3659 from mirpedrol/fix-tests

3011a2c

Update nf-core modules info command after meta.yml restructuring

Add pairgenomealign config to test cases for nf-core pipelines download.

c219b05

feat:download Eliminate known false positives also from direct matches.

9ff8fae

feat:config_parser Enable parsing of multi-line config values with ne…

e376521

…xtflow config --flat

[automated] Update CHANGELOG.md

c313e43

Handle empty string config values: Change regex to avoid catastrophic…

044e95b

… backtracking and assign them to the dict as well.

Set config value to null for empty values like it is done for paramet…

a9450f2

…ers parsed from main.nf

Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.2 (#3661)

61ea1c5

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

fix wrong key when updating module outputs

6a4bd33

[automated] Update CHANGELOG.md

f1e6650

renovate bot and others added 4 commits July 8, 2025 08:16

Merge pull request #3665 from mirpedrol/fix-lint-fix

06f48ff

Fix wrong key when updating module outputs

Merge branch 'main' into dev

ed96eed

downgrade to nf-version 24.10.5 (#3667)

6ebf39b

Co-authored-by: nf-core-bot <core@nf-co.re>

mirpedrol reviewed Jul 8, 2025

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mirpedrol reviewed Jul 8, 2025

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mashehu changed the title ~~Dev -> main for 3.4.0~~ Dev -> main for 3.3.2 Jul 8, 2025

mirpedrol approved these changes Jul 8, 2025

View reviewed changes

bump version to 3.3.2 (#3666)

e1cc6c9

mashehu enabled auto-merge July 8, 2025 09:21

mashehu merged commit 83a86a3 into main Jul 8, 2025
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Dev -> main for 3.3.2 #3664

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mashehu commented Jul 8, 2025

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Dev -> main for 3.3.2 #3664

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mashehu commented Jul 8, 2025

PR checklist

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