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Add CAT_SUMMARY process and offical_taxonomy param#366

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d4straub merged 8 commits intonf-core:devfrom
prototaxites:cat_summarise
Dec 16, 2022
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Add CAT_SUMMARY process and offical_taxonomy param#366
d4straub merged 8 commits intonf-core:devfrom
prototaxites:cat_summarise

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@prototaxites prototaxites commented Dec 6, 2022 •
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Added a CAT_SUMMARY process to summarise the output of CAT as a single final file, as currently there is a single output per assembly group (a lot if you have many single-sample assemblies!). I wanted to re-use the COMBINE_TSV process (as I essentially re-wrote it before realising it exists), but the output files from CAT are gzipped so I've cloned it and added an ungzipping line, rather than modify either the CAT output or push all the files through the GUNZIP process. I don't like duplicating code but this seemed like the simplest solution.

Also added an option to make CAT only output 'official' taxonomy, i.e. Kingdom, Phylum, etc. - I noticed this was available in the CAT documentation and thought it would be useful, as currently munging the taxonomy with many mismatched and empty fields is quite annoying!

Haven't run any tests yet as I've got a pipeline running on our cluster where I have the database downloaded (I don't think CAT will run on Gitpod?), but will un-draft this once I've had a chance to run a test/if anyone else wants to run a quick test.

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/mag 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 Dec 6, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7b0adf6

+| ✅ 148 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   7 tests failed       |-
Details

❌ Test failures:

❗ Test warnings:

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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.1
  • Run at 2022-12-16 11:32:44

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prototaxites commented Dec 6, 2022

@nf-core-bot fix linting

@prototaxites prototaxites marked this pull request as ready for review December 15, 2022 16:46
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prototaxites commented Dec 15, 2022

Finally got a chance to test this on our cluster - all working fine now.

d4straub
d4straub approved these changes Dec 16, 2022
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Looks good to me.
I also restarted test runs because they seem to have failed due to connectivity problems. Linting is expected to fail because of the template update.
In case all test pass (except linting) but you cannot merge the PR, ping me and I'll do it.

Comment thread conf/test.config Outdated
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prototaxites commented Dec 16, 2022

@d4straub All passing except linting as well - could you merge? Many thanks!

@d4straub d4straub merged commit 9ad1729 into nf-core:dev Dec 16, 2022
@prototaxites prototaxites deleted the cat_summarise branch December 20, 2022 11:23
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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