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modify template to use nf-validation plugin#1771

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mirpedrol wants to merge 66 commits intonf-core:devfrom

mirpedrol:schema-validation

Commits on Feb 23, 2023

Commits on May 16, 2023

Commits on May 22, 2023

update plugin version
mirpedrol
committed

Commits on May 23, 2023

Commits on May 25, 2023

Commits on May 26, 2023

Commits on May 30, 2023

Commits on Jun 5, 2023

Add -t / --tower option to 'nf-core download'.

MatthiasZepper
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mirpedrol
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Intermediate commit

MatthiasZepper
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Implement logic for the Tower download in DownloadWorkflow:download_workflow()

MatthiasZepper
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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.

MatthiasZepper
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Create WorkflowRepo subclass of ModuleRepo and initialise local clone.

MatthiasZepper
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TypeError: HEAD is a detached symbolic reference as it points to ...

MatthiasZepper
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Split history ./modules/modules_repo.py to synced_repo.py

MatthiasZepper
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Split history ./modules/modules_repo.py to synced_repo.py

MatthiasZepper
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mirpedrol
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Split history ./modules/modules_repo.py to synced_repo.py

MatthiasZepper
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Duplication of ModulesRepo to SyncedRepo done.

MatthiasZepper
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Strip ModulesRepo class of the methods moved to new superclass.

MatthiasZepper
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Rebase to current dev.

MatthiasZepper
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Local caching of the repo works now.

MatthiasZepper
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Started implementing the config download.

MatthiasZepper
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Started to implement the multiple revision selection for the Tower download.

MatthiasZepper
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Rewrite get_revision_hash() function to accomodate multiple revisions.

MatthiasZepper
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The 2nd revivial of the config choice. Now available for archives with only one revision.

MatthiasZepper
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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.

MatthiasZepper
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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…

MatthiasZepper
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Finished updating the prompts for the dialogues.

MatthiasZepper
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Converted the self.wf_download_url into a dict.

MatthiasZepper
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Enable multi-revision classic download.

MatthiasZepper
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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.

MatthiasZepper
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Initialise the Git repo clone of the workflow.

MatthiasZepper
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WorkflowRepo attributes and functions.

MatthiasZepper
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Finished the Tower download branch.

MatthiasZepper
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Minor tweaks to the container download functionality.

MatthiasZepper
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Updating docs and changelog, fixing linting errors.

MatthiasZepper
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Hopefully fixed the existing tests. New ones still need to be written.

MatthiasZepper
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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.

MatthiasZepper
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Add interactive check in retry for parsing the index.

MatthiasZepper
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Incorporating some suggestions by @mashehu.

MatthiasZepper
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Apply suggestions from code review @mashehu

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Writing additional tests for the --tower download functionality.

MatthiasZepper
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Move alterations from Version 2.8 (which this PR didn't make anymore) to Version 2.9dev.

MatthiasZepper
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Adding the info about remote containers to the summary log rather than showing it separately.

MatthiasZepper
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Moved the notification about remote containers to summary_log.

MatthiasZepper
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Apply suggestions from code review

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Fixes suggested by @mirpedrol during review. Thanks!

MatthiasZepper
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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…

MatthiasZepper
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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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rm dockerfile + add citations

SusiJo
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rm outdated Dockerfile

SusiJo
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add version and subpath to multiqc report comment link

mashehu
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update changelog

mashehu
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also add version to main link

mashehu
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fix linting test

mashehu
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update multiqc_config during version bump

mashehu
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bump version in multiqc_config correctly

mashehu
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