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Download pipelines for Tower#2247

Merged

MatthiasZepper merged 43 commits intonf-core:devfrom

MatthiasZepper:DownloadForTower

Jun 1, 2023

Commits on May 25, 2023

Add -t / --tower option to 'nf-core download'.
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Intermediate commit
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Implement logic for the Tower download in DownloadWorkflow:download_workflow()
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Extend ModulesRepo:setup_local_repo() with a cache_only bool, so we can use ModuleRepo as superclass to the new WorkflowRepo.
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Create WorkflowRepo subclass of ModuleRepo and initialise local clone.
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TypeError: HEAD is a detached symbolic reference as it points to ...
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Split history ./modules/modules_repo.py to synced_repo.py
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Split history ./modules/modules_repo.py to synced_repo.py
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Split history ./modules/modules_repo.py to synced_repo.py
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Duplication of ModulesRepo to SyncedRepo done.
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Strip ModulesRepo class of the methods moved to new superclass.
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Rebase to current dev.
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Local caching of the repo works now.
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Started implementing the config download.
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Started to implement the multiple revision selection for the Tower download.
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Rewrite get_revision_hash() function to accomodate multiple revisions.
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The 2nd revivial of the config choice. Now available for archives with only one revision.
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Inclusion of the revision in the output file name is problematic with the new ability to download multiple revisions at once. This resulted in loooooooong filenames.
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Allow multiple instances of the -r argument. Needed for scripted download. Ultimately, this now means that I also have to implement multiple version downloads for the classic download. Just downloa…
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Finished updating the prompts for the dialogues.
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Converted the self.wf_download_url into a dict.
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Enable multi-revision classic download.
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Small tweaks to ensure that tools doesn't bail out if there is no symlink from singularity to apptainer on the system.
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Initialise the Git repo clone of the workflow.
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WorkflowRepo attributes and functions.
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Finished the Tower download branch.
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Minor tweaks to the container download functionality.
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Updating docs and changelog, fixing linting errors.
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Hopefully fixed the existing tests. New ones still need to be written.
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Refactor the CLI commands for the Singularity Cache Dir
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Readme updates for the new remote Singularity cache feature.
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Add interactive check in retry for parsing the index.
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Incorporating some suggestions by @mashehu.
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Apply suggestions from code review @mashehu

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mashehu
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Writing additional tests for the --tower download functionality.
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Move alterations from Version 2.8 (which this PR didn't make anymore) to Version 2.9dev.
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Adding the info about remote containers to the summary log rather than showing it separately.
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Moved the notification about remote containers to summary_log.
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Apply suggestions from code review

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mashehu
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Fixes suggested by @mirpedrol during review. Thanks!
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@mashehu suggested that downloading the containers should not be optional for Tower downloads. Given that there is the option to provide the list of remote containers to skip their download, I agre…
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Commits on May 26, 2023

Bugfix: WorkflowRepo.tidy_tags() did indeed only tidy tags. However, revisions may also be branches. Therefore, I rewrote this function to account for revisions that are not releases.
MatthiasZepper
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Commits on May 31, 2023

Merge branch 'dev' into DownloadForTower
MatthiasZepper
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