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Add singularity.libraryDir to config page #5498

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Add singularity.libraryDir to config page #5498

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77e73ee
Add singularity.libraryDir to config page
christopher-hakkaart Nov 12, 2024
0ce806e
Update Apptainer and add versioned notes
christopher-hakkaart Nov 12, 2024
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4 changes: 2 additions & 2 deletions docs/container.md
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ This feature requires the `apptainer` tool to be installed where the workflow ex
Nextflow caches those images in the `apptainer` directory in the pipeline work directory by default. However it is suggested to provide a centralised cache directory by using either the `NXF_APPTAINER_CACHEDIR` environment variable or the `apptainer.cacheDir` setting in the Nextflow config file.

:::{versionadded} 21.09.0-edge
When looking for a Apptainer image file, Nextflow first checks the *library* directory, and if the image file is not found, the *cache* directory is used s usual. The library directory can be defined either using the `NXF_APPTAINER_LIBRARYDIR` environment variable or the `apptainer.libraryDir` configuration setting (the latter overrides the former).
Nextflow first checks the library directory when retrieving Apptainer images. The cache directory is used if the image file is not found. The library directory can also be defined using the `NXF_APPTAINER_LIBRARYDIR` environment variable. The `apptainer.libraryDir` configuration option overrides `NXF_APPTAINER_LIBRARYDIR` environment variable if both are set.
:::

:::{warning}
Expand Down Expand Up @@ -652,7 +652,7 @@ The `library://` pseudo-protocol allows you to import Singularity images from a
Nextflow caches the images in `${NXF_WORK}/singularity` by default. However, it is recommended to define a centralised cache directory using either the `NXF_SINGULARITY_CACHEDIR` environment variable or the `singularity.cacheDir` setting in the Nextflow config file.

:::{versionadded} 21.09.0-edge
When looking for a Singularity image file, Nextflow first checks the *library* directory, and if the image file is not found, the *cache* directory is used as usual. The library directory can be defined either using the `NXF_SINGULARITY_LIBRARYDIR` environment variable or the `singularity.libraryDir` configuration setting (the latter overrides the former).
Nextflow first checks the library directory when retrieving Singularity images. The cache directory is used if the image file is not found. The library directory can also be defined using the `NXF_SINGULARITY_LIBRARYDIR` environment variable. The `singularity.libraryDir` configuration option overrides `NXF_SINGULARITY_LIBRARYDIR` environment variable if both are set.
:::

:::{warning}
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14 changes: 14 additions & 0 deletions docs/reference/config.md
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Expand Up @@ -52,6 +52,13 @@ The following settings are available:
`apptainer.envWhitelist`
: Comma separated list of environment variable names to be included in the container environment.

`apptainer.libraryDir`
: Directory where remote Apptainer images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.

:::{versionadded} 21.09.0-edge
Nextflow first checks the library directory when retrieving Apptainer images. The cache directory is used if the image file is not found. The library directory can also be defined using the `NXF_APPTAINER_LIBRARYDIR` environment variable. The `apptainer.libraryDir` configuration option overrides `NXF_APPTAINER_LIBRARYDIR` environment variable if both are set.
:::

`apptainer.noHttps`
: Pull the Apptainer image with http protocol (default: `false`).

Expand Down Expand Up @@ -1375,6 +1382,13 @@ The following settings are available:
`singularity.envWhitelist`
: Comma separated list of environment variable names to be included in the container environment.

`singularity.libraryDir`
: Directory where remote Singularity images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.

:::{versionadded} 21.09.0-edge
Nextflow first checks the library directory when retrieving Singularity images. The cache directory is used if the image file is not found. The library directory can also be defined using the `NXF_SINGULARITY_LIBRARYDIR` environment variable. The `singularity.libraryDir` configuration option overrides `NXF_SINGULARITY_LIBRARYDIR` environment variable if both are set.
:::

`singularity.noHttps`
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it should be added an entry for apptainer.libraryDir as well.

Also the description could be extended to make it coherent with the explanation here

When looking for a Singularity image file, Nextflow first checks the library directory, and if the image file is not found, the cache directory is used as usual. The library directory can be defined either using the NXF_SINGULARITY_LIBRARYDIR environment variable or the singularity.libraryDir configuration setting (the latter overrides the former).

: Pull the Singularity image with http protocol (default: `false`).

Expand Down