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Important! Template update for nf-core/tools v2.13.1#599

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jfy133 merged 25 commits intodevfrom
nf-core-template-merge-2.13.1
May 6, 2024
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Important! Template update for nf-core/tools v2.13.1#599
jfy133 merged 25 commits intodevfrom
nf-core-template-merge-2.13.1

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@nf-core-bot nf-core-bot commented Mar 1, 2024

Version 2.13.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.13.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.13.1 release page.

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jfy133 commented Mar 26, 2024 •
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OK I've started this now, things that I will need to re-add back in once I've done the template merge bit:

TODO

  • Move contents of INPUT_CHECK to new subworkflow, check that output channels (raw_short, raw_long etc.) are prepared correctly
    • All --input validation code
    • Also include // Ensure run IDs are unique within samples (also prevents duplicated sample names)
    • All --assembly_input validation code
  • Move all input validation in lib/ to the new subworkflow
    • Update citation string at citation() function (can't remmeber wher enow) to include official mag one -> Already added in template!
    • Move validation from WorkflowMag.nf to validateInputPArametes
    • Update email sending to include busco_failed_bins(?) -> OPTED AGAINST THIS!
  • Re-add the citation text that in mag.nf get's appended to the end of the paramsSummaryLog()
  • Check input file existence still working (likely will need nextflow_schema.json update)
  • Make schema input for assembly input

Important

Must document/announce no more direct input!

Tests

General

  • Normal test ✅
  • Without run column ✅
  • Without group column ✅
  • Single end run ✅
  • long read (hybrid) test ✅

Error tests

Standard input

  • ✅ sr1 exists
  • ✅ sr2 exists
  • ✅ lr exists -> I guess it doesn't need to, just automatically runs short read only (no hybrid)(
  • run column exists and is not empty (i.e., can't be empty string)
    • ✅ get error if duplicate sample_id but no run id
  • ✅ sr1 is required column
  • ✅ if sr2, sr1 also required
  • ✅ if lr, sr1 and sr2 also required
  • ✅ if no sr2, --single_end is required -> tried to run with an empty R1
  • ✅ if sr2, --single_end MUST NOT be specified

Test input files:
template-merge-input-tests.zip

Test assembly input files:

template-merge-tests-assemblyinput.zip

Assembly input:

  • ✅ --assembly_input can only be used if --input supplied
  • ✅ FASTA column must not be empty
  • ✅ Assembly must not be empty (presumably one of supported)
  • ✅ IDs between --assembly_input and --input must match
    • ✅ also during coassembly

Other issues:

  • ✅ in validateInputParameters how to deal with the odd hybrid variable -> [FIXED] do the same as in current version (i.e., update the hybird variable that is defined in the main script, from wtihin a map{})

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github-actions Bot commented Mar 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41e8956

+| ✅ 212 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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 ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-06 09:00:43

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jfy133 commented Apr 19, 2024 •
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  1. I'm opting against adding the busco_failed_bins to the email, users would discover this by looking at the results, and now we have checkM etc. which we dont' get the report it seems unnecessarily specific.

It will reduce the load during future template merges

  1. Removing the custom check that --input must be suppilied if --assembly_input supplied, as --input is always required

jfy133
jfy133 reviewed Apr 19, 2024
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jfy133 reviewed Apr 19, 2024
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jfy133 reviewed Apr 19, 2024
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maxulysse
maxulysse reviewed Apr 30, 2024
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maxulysse reviewed Apr 30, 2024
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maxulysse
maxulysse approved these changes Apr 30, 2024
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minor comments, looking good

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CarsonJM commented Apr 30, 2024

Just went through the code/ran some tests and this update looks great! Would probably be worth adding a test_assembly_input profile, but that can probably be added when we implement nf-test

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jfy133 commented May 6, 2024

The failure on the test_binrefinement test is apparently a gzipped FASTA file is getting through to cONCOCT cut-up-contigs and the python tool can't read GZIPPEd files

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jfy133 commented May 6, 2024

Fixed, finallY! 🤞 all good!

@jfy133 jfy133 merged commit 8392af9 into dev May 6, 2024
@jfy133 jfy133 deleted the nf-core-template-merge-2.13.1 branch May 6, 2024 09:28
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@maxulysse maxulysse maxulysse approved these changes

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