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Added Minimap2 alignment #1486

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EgorGuga
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Updated version of pull-request #1459

Overview

In this pull-reqest, we added the ability to align reads using the minimap2 tool. The use of the tool is justified by the fact that this tool is popular and is used in commercial solutions, particularly in MegaBOLT.

P.S.
As long as the sort_bam variable is hardcoded as true a call of the minimap2 tool will not cause any problems.

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/sarek 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 Apr 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e91e972

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-10 14:13:36

@maxulysse maxulysse added this to the 3.5 milestone May 7, 2024
@maxulysse maxulysse changed the title Added Minimap2 alignment (3.4.1) Added Minimap2 alignment May 7, 2024
@maxulysse
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@nf-core-bot fix linting pretty please 🙏

@EgorGuga
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EgorGuga commented Jun 5, 2024

Please test with the last commit

@maxulysse
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Thanks for the efforts @EgorGuga

@maxulysse
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@nf-core-bot fix linting pretty please 🙏

asp8200
asp8200 reviewed Jun 10, 2024
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docs/usage.md
| mappability | ControlFREEC | http://xfer.curie.fr/get/vyIi4w8EONl/out100m2_hg38.zip | http://boevalab.inf.ethz.ch/FREEC/tutorial.html |
| minimap2 | Minimap2 | minimap2 -x sr -d ${fasta.baseName} $fasta | |
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Suggested change
| minimap2 | Minimap2 | minimap2 -x sr -d ${fasta.baseName} $fasta | |
| minimap2 | Minimap2 | `minimap2 -x sr -d ${fasta.baseName} $fasta` | |

asp8200
asp8200 reviewed Jun 10, 2024
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nextflow_schema.json
@@ -733,6 +733,13 @@
"hidden": true,
"help_text": "If you use AWS iGenomes, this has already been set for you appropriately."
},
"minimap2": {
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I would have named that parameter minimap2_index.

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I think we have bwa and bwamem2, so I'm happy with just minimap2

@FriederikeHanssen FriederikeHanssen removed this from the 3.5 milestone Aug 19, 2024
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@maxulysse maxulysse maxulysse left review comments

@asp8200 asp8200 asp8200 left review comments

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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5 participants
@EgorGuga @maxulysse @asp8200 @FriederikeHanssen @nf-core-bot