Milad Miladi

Hello, It seems that numpy is needed for setting up installation with pip, otherwise the pip installer complains with: ``` Cache entry deserialization failed, entry ignored Using cached https://files.pythonhosted.org/packages/ce/41/99b51880c9d9835218978008cf75851f2257f9fe0271e5d76c96b17fe501/poreplex-0.4.tar.gz Complete...

missing bed files

3

Hi @hyeshik , First of all, thanks much for your efforts and this neat, thorough and transparent work. I managed to run the *reference* snakemake workflow, but for the *nanopore*...

Issues and ideas for improving GraphClust wrappers

2

Below I collect a list of issues to resolve and points to improve with GraphClust wrappers. This issue is intended to collect them in the first place, rather than fixing...

Guppy software version for base calling

1

Hello, Thanks for providing this tool! I was wondering if the version of Guppy can have an impact on the prediction quality and performance. I have data called using Guppy...

Question about eventalign parallelization at file level

5

Hi, Is it possible to speedup eventalign computations by splitting the files and/or region windowing? For example to speedup `nanopolish eventalign --reads all.fastq --bam all.bam --genome genome.fa > all.tsv`, split...

Eventalign: multi-threading does not function for the conda version

7

Hi, The conda binary ignores the thread option for `eventalign` mode (at least). I could verify that the git-make-based installation runs with the palatalization on the same system. So there...

Help for using the proper metric for each mode

4

Hi, The diversity of available detection modes and the `text_out` types, makes it a bit difficult to grasp an overview of the recommended modification detection metrics for each mode. I...

Warn if `.shed.yml` is not available for the tool

2

Hi, It might worth to have an automatic sanity check for the existence of `.shed.yml` file for `planemo test/lint tool.xml` This could help for not missing the tool during CI...