Andrew Beggs comments

Results 27 comments of


                                            Andrew Beggs

"Precondition Failed [412]" error on every sync

Hi Paul. Thanks for the useful tool. Having the same issue as everyone else. Have attached the logfile if it helps Many thanks Andrew [OGcalsync.log](https://github.com/phw198/OutlookGoogleCalendarSync/files/6793466/OGcalsync.log)

Request: Cohort analysis

I think similar to maftools - which I have used as well. Your report is very close to the one that the 100,000 Genomes project produces in the UK and...

Request: Cohort analysis

[testcnv.zip](https://github.com/sigven/pcgr/files/3828372/testcnv.zip) Sure - try this - it is from the Illumina Canvas caller. I've been using your pipeline for Nanopore Promethion WGS data too and it works well!

Request: Cohort analysis

Also, SV integration would also be useful - we've used Manta for Illumina calls and Sniffles for Nanopore... happy to supply data from these as well. We've tried to write...

pple64 support for minimap2

I can now see that others have requested the same - I would be happy to set up access to our power9 nodes if it helps?

NanoSV doesn't play nicely with guppy BAM file output

Yep

ERROR ~ Cannot invoke method startsWith() on null object

Sure: ``` //Profile config names for nf-core/configs singularity { enabled = true autoMounts = true } process { executor = 'slurm' } params { max_memory = 128.GB max_cpus = 32...

ERROR ~ Cannot invoke method startsWith() on null object

Hmm I see exactly the same on 3.1.4 when I removed the latest version and download the last version it worked on.. must be the sample sheet but it looks...

TypeError: filename expected str, os.PathLike or fsspec.OpenFile, got: u'/data/cm/soapswga/gemomes/cpar_genome.fasta'

Just to note I have solved this issue, which was caused by a too up to date version of pafaidx - if you downgrade the version of pyfaidx as below...

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

Hi Sigve I have got a NA12878 genome sequencer somewhere so let me run the pipeline on it and I can attached the SVs, CNVs etc on it. Will take...