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expose bwa mem -T parameter #159

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ivokwee opened this issue Jun 9, 2020 · 2 comments
Closed

expose bwa mem -T parameter #159

ivokwee opened this issue Jun 9, 2020 · 2 comments
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feature-request Request to add new functionality

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@ivokwee
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ivokwee commented Jun 9, 2020

Hi. I had a case that I needed to lower the score threshold of BWA-mem. The default is T=30 but all reads were filtered out and I had to set the T=15. Can we expose the T option in the nextflow run options?
@drpatelh
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drpatelh commented Jun 9, 2020

Hi @ivokwee. Sounds like a reasonable request. Was there a reason as to why the alignments had low scores? We could either add a generic parameter e.g. --alignment_options or a specific one to tweak that particular option e.g. --alignment_score. Using the former would be much easier to integrate with Nextflow DSL 2 which is not far off now for this pipeline.

@drpatelh drpatelh added the feature-request Request to add new functionality label Jun 9, 2020
drpatelh added a commit to drpatelh/nf-core-chipseq that referenced this issue Jul 1, 2020
@drpatelh
Fix nf-core#159
15fa2fe
@drpatelh
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drpatelh commented Jul 1, 2020

Fixed here @ivokwee. Thanks for reporting!

@drpatelh drpatelh closed this as completed Jul 1, 2020
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