Refactor pipeline downloads command to use nextflow inspect for container detection
#3634
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@@ -61,7 +61,7 @@ | |
| ) | ||
| from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows | ||
| from nf_core.components.constants import NF_CORE_MODULES_REMOTE | ||
| from nf_core.pipelines.download.download import DownloadError | ||
| from nf_core.pipelines.list import autocomplete_pipelines | ||
| from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir | ||
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@@ -400,33 +400,33 @@ def command_pipelines_lint( | |
| @click.option( | ||
| "-s", | ||
| "--container-system", | ||
| type=click.Choice(["none", "singularity", "docker"]), | ||
| help="Download container images of required software.", | ||
| ) | ||
| @click.option( | ||
| "-l", | ||
| "--container-library", | ||
| multiple=True, | ||
| help="Container registry/library or mirror to pull images from. Not available for Docker containers.", | ||
| ) | ||
| @click.option( | ||
| "-u", | ||
| "--container-cache-utilisation", | ||
| type=click.Choice(["amend", "copy", "remote"]), | ||
| help="Utilise a `singularity.cacheDir` in the download process, if applicable. Not available for Docker containers.", | ||
| ) | ||
| @click.option( | ||
| "-i", | ||
| "--container-cache-index", | ||
| type=str, | ||
| help="List of images already available in a remote `singularity.cacheDir`. Not available for Docker containers.", | ||
| ) | ||
| @click.option( | ||
| "-d", | ||
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There was a problem hiding this comment. I think, @mirpedrol and @mashehu are quite strict on renaming existing CLI arguments, since breaking changes would, according to SemVer, require a new major version release (4.0.0). But maybe Click would map a Apart from that, CLI parameters in download are mostly standardized in a way that the first letter of the last term is their short flag: What was the reason you wish to rename? As far as I remember, it used to be There was a problem hiding this comment. I think we can be sloppy enough to see a long name change of a parameter not as a breaking change, especially if it is just because of semantics 🙂 There was a problem hiding this comment. I agree with this. I wouldn't change unless there is a good reason to. There was a problem hiding this comment. Fair. But particularly because there is a short flag, I also do not necessarily see the need to abbreviate the long form. But that is not a hill to die on for me, so have it as you like. There was a problem hiding this comment. Do as you see fit, I will also not fight anyone on this :) There was a problem hiding this comment. joining late to the party, but I would vote for keeping the long There was a problem hiding this comment. In the interest of not changing the API I think I agree with you and others @mirpedrol -- I'll switch back the change. I think Julians suggestion with There was a problem hiding this comment. I think we decided to not use There was a problem hiding this comment. At NGI, we continue calling it Tower, since Platform is simply a more cumbersome generic name. But I doubt that many will still remember the old parameters - judged by the Slack discussions, very few people ever used that functionality anyway. So fine with me. There was a problem hiding this comment. I see -- slightly annoying then that platform/tower perfectly cover the two normal parallelism short flags... I've reverted the change now 👍 |
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| "--parallel", | ||
| type=int, | ||
| default=4, | ||
| help="Number of allowed parallel tasks", | ||
| ) | ||
| @click.pass_context | ||
| def command_pipelines_download( | ||
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@@ -443,7 +443,7 @@ def command_pipelines_download( | |
| container_library, | ||
| container_cache_utilisation, | ||
| container_cache_index, | ||
| parallel, | ||
| ): | ||
| """ | ||
| Download a pipeline, nf-core/configs and pipeline singularity images. | ||
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@@ -462,7 +462,7 @@ def command_pipelines_download( | |
| container_library, | ||
| container_cache_utilisation, | ||
| container_cache_index, | ||
| parallel, | ||
| ) | ||
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@@ -2359,7 +2359,7 @@ def command_create_params_file(pipeline, revision, output, force, show_hidden): | |
| @click.option( | ||
| "-s", | ||
| "--container-system", | ||
| type=click.Choice(["none", "singularity", "docker"]), | ||
| help="Download container images of required software.", | ||
| ) | ||
| @click.option( | ||
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