Andrew Beggs

pple64 support for minimap2

2

Hi Thanks for this great bit of software. I know it sounds like a funny request but I would like to compile minimap2 on our power9 GPU nodes - essentially...

Request: Cohort analysis

9

Thanks for the great tool - very useful! Do you think there would be any chance of a summary HTML across a cohort of samples that have been through PCGR?

### Name of the tool ONT Minknow ### Tool homepage https://nanoporetech.com/about-us/news/introducing-new-minknow-app ### Tool description ONT Sequencing processing ### Tool output [reports.tar.gz](https://github.com/ewels/MultiQC/files/13437925/reports.tar.gz) ### Log filename pattern _No response_ ### Data suitable...

ERROR ~ Cannot invoke method startsWith() on null object

6

### Description of the bug I've just upgraded sarek from 3.14 to the latest version. When I run it now it crashes out almost immediately with: `ERROR ~ Cannot invoke...

Feature request: Compatibility with Starlong

9

Hi I am trying to do fusion neoantigen prediction using Arriba, however STAR can't cope with long reads and ideally STARlong should be used - do you think this will...

Incorrect parameter passing causes segmentation fault

1

Hi More of an observation that I don't read instructions properly but if you pass --minmaf instead of --minMAF to cellsnp-lite it dumps with a segmentation fault. Ditto for --minCOUNT...

Can't upload more than 99 samples at a time

8

Hi Great tool - but every time I try to upload more than 99 samples I get an error: Unable to read report files from directory /tmp/RtmpCimO7C/6d2f48dfad781b742e6064d5. I've tried uploading...

Does not generate HTML or TSV files at all

1

Hi Thanks for the fantastic bit of software. I have aggregated ~250 Kraken2 reports, and it seems to visualise just fine. However trying to output a HTML file or TSV...

Genotyping amplicons?

1

Hi, Thanks for a great tool. I am playing around with genotyping amplicon data from Nanopore sequencing. I can get Straglr to call certain STRs but not others, and I...

Feature Request - support CNV calls (and ideally SV calls)

2

HI all Self explanatory hopefully. We have got a germline adaptive sampling panel working on Nanopore, and are generating copy number variants and SVs (including fusions) - do you think...