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Fix typos
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ewels committed Mar 18, 2024
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8 changes: 4 additions & 4 deletions README.md
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Expand Up @@ -376,7 +376,7 @@ The pipeline files are automatically updated (`params.custom_config_base` is set
So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs).

> [!WARNING]
> This option is not available when downloading a pipeline for use with [Sqerea Platform](#adapting-downloads-to-seqera-platform) because the application manages all configurations separately.
> This option is not available when downloading a pipeline for use with [Seqera Platform](#adapting-downloads-to-seqera-platform) because the application manages all configurations separately.
### Downloading Apptainer containers

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### Adapting downloads to Seqera Platform

[Seqera Platform](https://seqera.io/platform/) (formerly _"Nextflow Tower"_) provides a graphical user interface to oversee pipeline runs, gather statistics and configure compute resources. While pipelines added to _Seqerea Platform_ are preferably hosted at a Git service, providing them as disconnected, self-reliant repositories is also possible for premises with restricted network access. Choosing the `--platform` flag will download the pipeline in an appropriate form.
[Seqera Platform](https://seqera.io/platform/) (formerly _"Nextflow Tower"_) provides a graphical user interface to oversee pipeline runs, gather statistics and configure compute resources. While pipelines added to _Seqera Platform_ are preferably hosted at a Git service, providing them as disconnected, self-reliant repositories is also possible for premises with restricted network access. Choosing the `--platform` flag will download the pipeline in an appropriate form.

Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Seqerea Platform_ using the `file:/` prefix.
Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Seqera Platform_ using the `file:/` prefix.

> [!TIP]
> Also without access to Seqerea Platform, pipelines downloaded with the `--platform` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
> Also without access to Seqera Platform, pipelines downloaded with the `--platform` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
## Pipeline software licences

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1 change: 1 addition & 0 deletions nf_core/__main__.py
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Expand Up @@ -358,6 +358,7 @@ def create_params_file(pipeline, revision, output, force, show_hidden):
help="Archive compression type",
)
@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files")
# TODO: Remove this in a future release. Deprecated in March 2024.
@click.option(
"--tower",
is_flag=True,
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