Minibwa speedup

[ignacio3437]

Updating bwa-index and bwa-mem to minibwa-index and minibwa-map.

Running the full HY hic dataset results in significant speedups from 11 H 10min to 6 H 20 min to run the full pipeline. The heatmaps look idential although the relutling bam files are not identical as evident from the hicqc.

I am having major issues with the nf-core linting steps even though I installed the module using nf-core modules install. Will need some help there to get the pipeline to lint, but it seems to run fine. I'm also not able to run the tests to update the snapshots on my WSL laptop. Is it possible to do this on PP?

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
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes: nextflow run . -profile test,docker --outdir <OUTDIR> and nf-test test --profile docker tests/.
• 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).

[github-actions]

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• This CI test will remain failed until you push a new commit

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Hi @ignacio3437,

It looks like this pull-request is has been made against the ignacio3437/assemblyqc main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the ignacio3437/assemblyqc dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[ignacio3437]

See results here:
MiniBWA_Tests.pdf

[GallVp]

@ignacio3437

Great work. That's a big improvement. Let me take care of the merge.

[GallVp]

container 'docker.io/gallvp/haphic:1.0.7--hdfd78af_0'

This is adequate for both singularity and docker.

[GallVp]

I'll get to it after GallVp/nxf-components#104

The upstream modules and sub workflows need an update. The modified sub workflow comes from nxf-components.