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Add entry point to pipeline at binning stage#439

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prototaxites merged 5 commits intonf-core:devfrom
prototaxites:binning_entry
May 17, 2023
Merged

Add entry point to pipeline at binning stage#439
prototaxites merged 5 commits intonf-core:devfrom
prototaxites:binning_entry

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@prototaxites prototaxites commented May 10, 2023 •
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Resolves #431. Hope the documentation is clear! Will create a separate PR in the test-datasets repo to add the assemblies and assembly samplesheet for the test config.

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 May 10, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f82bfa7

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ 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 2.8
  • Run at 2023-05-11 08:21:20

@prototaxites prototaxites mentioned this pull request May 10, 2023
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jfy133
jfy133 approved these changes May 11, 2023
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I think this looks good to me (a few documentation clarifications).

The code is getting rather complex now with many nested if/else statements, I think alot of this needs to be refactorered into more subworkflows as it's getting hard to read now... but that's for another time! Thanks @prototaxites - It hink this is going to be really popular functionality :)

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Comment thread nextflow_schema.json Outdated
Comment thread nextflow_schema.json Outdated
d4straub
d4straub reviewed May 11, 2023
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Comment thread workflows/mag.nf
d4straub
d4straub reviewed May 11, 2023
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Comment thread subworkflows/local/input_check.nf Outdated
@prototaxites prototaxites mentioned this pull request May 12, 2023
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@prototaxites prototaxites merged commit 3468737 into nf-core:dev May 17, 2023
@prototaxites prototaxites deleted the binning_entry branch May 17, 2023 08:21
@prototaxites prototaxites mentioned this pull request May 18, 2023
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@prototaxites prototaxites mentioned this pull request Jun 12, 2023
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@jfy133 jfy133 jfy133 approved these changes

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