Minibwa speedup - #325
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This PR is against the
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See results here: |
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Great work. That's a big improvement. Let me take care of the merge. |
| 'https://depot.galaxyproject.org/singularity/haphic:1.0.7--hdfd78af_0': | ||
| 'biocontainers/haphic:1.0.7--hdfd78af_0' }" | ||
| 'docker://gallvp/haphic:1.0.7--hdfd78af_0': | ||
| 'docker.io/gallvp/haphic:1.0.7--hdfd78af_0' }" |
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container 'docker.io/gallvp/haphic:1.0.7--hdfd78af_0'
This is adequate for both singularity and docker.
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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. |
2 participants
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
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>andnf-test test --profile docker tests/.nextflow run . -profile debug,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).