Eike Steinig

Coverage file error

1

Versions: * Python 3.9 * ISS 1.5.4 Reproduce: ``` echo -e "ref.fasta 0.1" > coverage.txt iss generate --cpus 4 --draft ref.fasta --model miseq --coverage_file coverage.txt --output pool_miseq ``` Error: ```...

This file check should have a space between the `!` and `-f` otherwise it breaks in `Nextflow` where the `bed` file is symlinked ```bash err("Can't read --bed $bed") if $bed...

It should work by adding a space, tested successfully.

TypeError: Cannot create property 'Run' on string ' '

1

I am running into the following error when searching the SRA for all *Staphylococcus aureus* sequences: ``` Command executed: bionode-ncbi search sra "Staphylococcus aureus" > results.txt Command exit status: 1...

Plotting is not in line with the minimal design approach of `nanoq`, but it may be useful to have access to per-read length and quality data.

Add a total input read field to report

Auto detection of compression when writing to `stdout` is currently not implemented. It can be activated when specifying the `--output-type|-O` argument. It would be better for consistency to enable auto...

At the moment empty files error due to `needletail` - implement a flag that allows for zero outputs

Ambiguous base filter

2

Requested by @mbhall88 - [ ] Remove reads with > x % ambiguous bases - [ ] Command line option for filter and allowed bases - [ ] Speed optimisation...