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Download: Improve container detection in configs, specifically the container parameter in process scope #2346

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Merged
mirpedrol merged 6 commits into from
Jun 30, 2023
Merged

Download: Improve container detection in configs, specifically the container parameter in process scope #2346

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6aa0b08
Split into two functions. This allows to use the DSL2 regexes also f…
MatthiasZepper Jun 28, 2023
766a639
WIP commit, refactoring regexes again, because well...there are also …
MatthiasZepper Jun 29, 2023
c7c19a2
Almost finished refactoring the container detection. Need to test edg…
MatthiasZepper Jun 29, 2023
ccbb131
Hopefully, refactoring of container detection is finished now. Dedupl…
MatthiasZepper Jun 29, 2023
fd3f641
Added a test, but realized that Sarek has yet another edge-case. Clea…
MatthiasZepper Jun 29, 2023
cdf620e
Add mock config for container detection.
MatthiasZepper Jun 29, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -28,6 +28,7 @@
- Refactored the CLI for `--singularity-cache` in `nf-core download` from a flag to an argument. The prior options were renamed to `amend` (container images are only saved in the `$NXF_SINGULARITY_CACHEDIR`) and `copy` (a copy of the image is saved with the download). `remote` was newly introduced and allows to provide a table of contents of a remote cache via an additional argument `--singularity-cache-index` ([#2247](https://github.com/nf-core/tools/pull/2247)).
- Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter `--singularity-cache-index` introduced in [#2247](https://github.com/nf-core/tools/pull/2247) has been renamed to `--container-cache-index` prior to release ([#2336](https://github.com/nf-core/tools/pull/2336)).
- To address issue [#2311](https://github.com/nf-core/tools/issues/2311), a new parameter `--container-library` was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled ([#2336](https://github.com/nf-core/tools/pull/2336)).
- Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes [#2346](https://github.com/nf-core/tools/pull/2346).

#### Updated CLI parameters

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