Added pharokka annotations and updated nf-tests to use nf-core/modules test data

[CarsonJM]

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/phageannotator 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>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

[CarsonJM]

Consistently running into issues because of no remaining storage. Should be fixed by nextflow-io/nextflow#4713

[jfy133]

Overall looks fine, is there any reason why you have so many local modules (the actual module files I can't see from my phone, so maybe they are very custom, but going to ask anyway)?

Once tested pass - node there are ways to delete random stuff on the gha node that isn't used for anything, if that helps... I can't remember who did it now but you could ask on slack

[CarsonJM]

Several of the local modules/subworkflows are very custom. But I have a to do list of adding many of them to nf-core modules. I'm also looking into potential nf-core module replacements for a few of them

#39

[jfy133]

You can give to includeConfig URLs as well as local paths: You already do this with importing institutional profiles https://github.com/nf-core/phageannotator/blob/dev/nextflow.config#L144 So I imagine you can just use the same concept for the test data file

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On Sat, 17 Feb 2024, 15:15 Carson J Miller, ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In conf/test_data.config <#92 (comment)> : > params { - // Base directory for test data - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/phageannotator" - modules_testdata_base_path = "s3://ngi-igenomes/testdata/nf-core/modules/" + // Base directories for test data + phageannotator_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/phageannotator" + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' I did just copy over the file because I wasn't aware of better options. I'm definitely open to alternatives! What would importing the file with the map itself look like? — Reply to this email directly, view it on GitHub <#92 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEI6MTYRMQ5I77PRX2TZ7XDYUC3QFAVCNFSM6AAAAABDAQ3FCKVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTQOBWGU3TQOJYG4> . You are receiving this because you commented.Message ID: ***@***.***>

[jfy133]

Ok, sounds good!

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On Sat, 17 Feb 2024, 15:22 Carson J Miller, ***@***.***> wrote: Several of the local modules/subworkflows are very custom. But I have a to do list of adding many of them to nf-core modules. I'm also looking into potential nf-core module replacements for a few of them #39 <#39> — Reply to this email directly, view it on GitHub <#92 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEI6MTZDWXGPOO3C7TDMJ5TYUC4J5AVCNFSM6AAAAABDAQ3FCKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJQGIZDEMZVGA> . You are receiving this because you commented.Message ID: ***@***.***>