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Add Info message and suggest adding detected libraries as arguments i…
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| Original file line number | Diff line number | Diff line change |
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@@ -13,7 +13,7 @@ | |
| ### Download | ||
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| - Improved container image resolution and prioritization of http downloads over Docker URIs ([#2364](https://github.com/nf-core/tools/pull/2364)). | ||
| - Explicit container registry specifications will be ignored, so registries provided with `-l`/`--container-library` are used instead. ([#2400](https://github.com/nf-core/tools/pull/2400)). | ||
| - Explicit container registry specifications will be ignored, so registries provided with `-l`/`--container-library` are used instead. ([#2403](https://github.com/nf-core/tools/pull/2403)). | ||
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| ### Linting | ||
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@@ -37,9 +37,9 @@ | |
| - `params.max_multiqc_email_size` is no longer required ([#2273](https://github.com/nf-core/tools/pull/2273)) | ||
| - Remove `cleanup = true` from `test_full.config` in pipeline template ([#2279](https://github.com/nf-core/tools/pull/2279)) | ||
| - Fix usage docs for specifying `params.yaml` ([#2279](https://github.com/nf-core/tools/pull/2279)) | ||
| - Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk] | ||
| - Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286) | ||
| - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287) | ||
| - Added stub in modules template ([#2277])(<https://github.com/nf-core/tools/pull/2277>) [Contributed by @nvnieuwk] | ||
| - Move registry definitions out of profile scope ([#2286])(<https://github.com/nf-core/tools/pull/2286>) | ||
| - Remove `aws_tower` profile ([#2287])(<https://github.com/nf-core/tools/pull/2287>) | ||
| - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291)) | ||
| - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298)) | ||
| - Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301)) | ||
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@@ -80,7 +80,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr | |
| ### Linting | ||
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| - Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270)) | ||
| - Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(https://github.com/nf-core/tools/pull/2278/files) | ||
| - Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(<https://github.com/nf-core/tools/pull/2278/files>) | ||
| - Detect if container is 'simple name' and try to contact quay.io server by default ([#2281](https://github.com/nf-core/tools/pull/2281)) | ||
| - Warn about null/None/empty default values in `nextflow_schema.json` ([#3328](https://github.com/nf-core/tools/pull/2328)) | ||
| - Fix linting when creating a pipeline skipping some parts of the template and add CI test ([#2330](https://github.com/nf-core/tools/pull/2330)) | ||
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@@ -111,7 +111,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr | |
| - 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 | ||
| - Updated AWS tests to use newly moved `seqeralabs/action-tower-launch` instead of `nf-core/tower-action` | ||
| - Remove `.cff` files from `.editorconfig` [(#2145)[https://github.com/nf-core/tools/pull/2145]] | ||
| - Remove `.cff` files from `.editorconfig` [[#2145](https://github.com/nf-core/tools/pull/2145)] | ||
| - Simplify pipeline README ([#2186](https://github.com/nf-core/tools/issues/2186)) | ||
| - Added support for the apptainer container engine via `-profile apptainer`. ([#2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by @jfy133] | ||
| - Added config `docker.registry` to pipeline template for a configurable default container registry when using Docker containers. Defaults to `quay.io` ([#2133](https://github.com/nf-core/tools/pull/2133)) | ||
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@@ -1138,7 +1138,7 @@ making a pull-request. See [`.github/CONTRIBUTING.md`](.github/CONTRIBUTING.md) | |
| - Move `params`section from `base.config` to `nextflow.config` | ||
| - Use `env` scope to export `PYTHONNOUSERSITE` in `nextflow.config` to prevent conflicts with host Python environment | ||
| - Bump minimum Nextflow version to `19.10.0` - required to properly use `env` scope in `nextflow.config` | ||
| - Added support for nf-tower in the travis tests, using public mailbox [email protected] | ||
| - Added support for nf-tower in the travis tests, using public mailbox <[email protected]> | ||
| - Add link to [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and [Semantic Versioning](http://semver.org/spec/v2.0.0.html) to CHANGELOG | ||
| - Adjusted `.travis.yml` checks to allow for `patch` branches to be tested | ||
| - Add Python 3.7 dependency to the `environment.yml` file | ||
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