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Add Unzipping deeparg db option #320

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Add Unzipping deeparg db option #320

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jfy133
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@jfy133 jfy133 commented Nov 8, 2023 •
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Needs testing! DeepARGi sn't working on my laptop atm for reasons unknown to me...

Please test:

  • Running with autodownload (although will fail)
  • Running with suppling a Zenodo downloaded ZIP
  • Running with an uncompressed database

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Nov 8, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/funcscan master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/funcscan dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from master to dev November 8, 2023 11:43
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github-actions bot commented Nov 8, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 103247c

+| ✅ 158 tests passed       |+
!| ❗   1 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/funcscan/tree/dev" target="_blank">nf-core/funcscan</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/funcscan/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/dev" target="_blank">nf-core/funcscan</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/funcscan/dev/docs/output" target="_blank">documentation</a>.

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-24 08:40:31

@jfy133 jfy133 requested a review from a team November 8, 2023 14:21
@jasmezz jasmezz self-requested a review November 9, 2023 11:03
jasmezz
jasmezz requested changes Nov 9, 2023
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I tested:

  • Running with autodownload – ❌ as expected because server down
  • Running with supplying a Zenodo downloaded ZIP – ✔️
  • Running with an uncompressed database – ✔️

Note: The ZIP file is a bit annoying, because it contains another folder (which is actually our required input) plus irrelevant MacOS system files. But it runs smoothly now with the pipeline.

subworkflows/local/arg.nf

if ( file(params.arg_deeparg_data).getExtension() == "zip") {
UNZIP( [ [id: "deepargdb"], params.arg_deeparg_data ] )
ch_deeparg_db = UNZIP.out.unzipped_archive.map{meta, db -> [db]}
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@jasmezz jasmezz Nov 9, 2023 •
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Suggested change
ch_deeparg_db = UNZIP.out.unzipped_archive.map{meta, db -> [db]}
ch_deeparg_db = UNZIP.out.unzipped_archive.map{meta, db -> db}
.flatMap { it -> [ it + "/deeparg"] }

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The Zip file on Zenodo is a bit annoying because it contains a subfolder /deeparg which is the actual input we want. Hence the .flatMap line.

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Hmm I don't like that solution in case someone has made their own zip in the correct manner... So appending that may not always work... I guess we need to make update the module to find a file within it like is done in other modules like bwa/bowtie2

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jfy133 and others added 2 commits November 10, 2023 14:51
@jfy133 @jasmezz
Update nextflow_schema.json
b2ece35 
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
@jfy133 @jasmezz
Update nextflow_schema.json
66cc1f3 
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
@jasmezz jasmezz mentioned this pull request Nov 16, 2023
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jfy133 commented Jan 24, 2024

@nf-core-bot fix linting

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jfy133 commented Jan 24, 2024

Closing as tool should deal with does this now itself

@jfy133 jfy133 closed this Jan 24, 2024
@jasmezz jasmezz deleted the unzip-deeparg-db-option branch February 27, 2024 18:49
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