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Merged
mirpedrol merged 4 commits into from
Apr 27, 2023
Merged

move misplaced changelog points #2259

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6887ac1
move misplaced changelog points
mirpedrol Apr 27, 2023
86f1368
Update CHANGELOG.md
mirpedrol Apr 27, 2023
6935f44
update changelog
mirpedrol Apr 27, 2023
d8d9cab
Merge branch 'changelog-fixes' of https://github.com/mirpedrol/tools …
mirpedrol Apr 27, 2023
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12 changes: 6 additions & 6 deletions CHANGELOG.md
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Expand Up @@ -4,10 +4,11 @@

### Template

- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))
- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
- Add a clean-up GHA which closes issues and PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
- Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by @Midnighter, @jfy133]
- Consistent syntax for branch checks in PRs ([#2202](https://github.com/nf-core/tools/issues/2202))
- Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
Expand All @@ -19,6 +20,7 @@
- Add tower.yml file to the pipeline template ([#2251](https://github.com/nf-core/tools/pull/2251))
- Add mastodon badge to README ([#2253](https://github.com/nf-core/tools/pull/2253))
- Removed `quay.io` from all module Docker container references as this is now supplied at pipeline level. ([#2249](https://github.com/nf-core/tools/pull/2249))
- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([#2059](https://github.com/nf-core/tools/pull/2059)).

### Linting

Expand All @@ -42,22 +44,23 @@

### General

- Deprecate Python 3.7 support because it reaches EOL ([#2210](https://github.com/nf-core/tools/pull/2210))
- `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)).
- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
- Add a clean-up GHA which closes issues and PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
- update minimum version of rich to 13.3.1 ([#2185](https://github.com/nf-core/tools/pull/2185))
- Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
- Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
- Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
- Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([#2228](https://github.com/nf-core/tools/pull/2228) [#2239](https://github.com/nf-core/tools/pull/2239)).
- Add the possibility to translate refgenie asset aliases to the ones used in a pipeline with an alias_translations.yaml file ([#2242](https://github.com/nf-core/tools/pull/2242)).
- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))

## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]

### Template

- Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114))
- Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132))
- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))

### Linting

Expand All @@ -69,7 +72,6 @@
- Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
- Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
- Handle `json.load()` exceptions ([#2134](https://github.com/nf-core/tools/pull/2134))
- Deprecate Python 3.7 support because it reaches EOL ([#2210](https://github.com/nf-core/tools/pull/2210))

## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]

Expand Down Expand Up @@ -102,8 +104,6 @@ Another big release with lots of new features and bug fixes. Thanks to all contr

- Fix lint warnings for `samplesheet_check.nf` module ([#1875](https://github.com/nf-core/tools/pull/1875)).
- Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))
- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([#2059](https://github.com/nf-core/tools/pull/2059)).- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))
- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))

### Linting

Expand Down