Added Minimap2 alignment #1486
Open
Added Minimap2 alignment #1486
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
|
@nf-core-bot fix linting pretty please 🙏 |
|
Please test with the last commit |
|
Thanks for the efforts @EgorGuga |
|
@nf-core-bot fix linting pretty please 🙏 |
maxulysse
reviewed
Jun 10, 2024
asp8200
reviewed
Jun 10, 2024
asp8200
reviewed
Jun 10, 2024
| @@ -733,6 +733,13 @@ | |||
| "hidden": true, | |||
| "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." | |||
| }, | |||
| "minimap2": { | |||
There was a problem hiding this comment.
I would have named that parameter minimap2_index.
There was a problem hiding this comment.
I think we have bwa and bwamem2, so I'm happy with just minimap2
<!-- # nf-core/sarek pull request Many thanks for contributing to nf-core/sarek! Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) --> ## 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](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/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).
|
@nf-core-bot fix linting pretty please 🙏 |
applied suggested change in docs/usage.md Co-authored-by: Anders Sune Pedersen <[email protected]>
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).