Josh Loecker

I'd like to start by saying thank you for putting this together - it's been working great! As the title states, would it be possible to add a second instance...

It would be nice to have a"-quiet" flag for a list of options to pass to phantom, and only show errors if any occur.

Unable to use caching in BioDBNet

1

Hello, I have an example below ```python from bioservices import BioDBNet net = BioDBNet(verbose=True, cache=True) ``` And I receive the following output ``` INFO [bioservices.BioDBNet:363]: Initialising BioDBNet service (REST) INFO...

Removing online backups

1

When using the `rclone` option, are the uploaded files also deleted after the `PRUNE_BACKUPS_DAYS` option?

Get multiple groups from type=match

1

### Behaviour I would like to select discontinuous portions of a tag, but it isn't possible using only regex #### Steps to reproduce this issue 1. Using this regex101 as...

Using pigz for parallel gzip operations

2

Hello, it is possible to use pigz for parallel gzip operations? I've allowed 10 threads for fastq_screen, but only a single thread is used for gzip. It would be super...

Unable to reach BioDBNet URL

1

Hi, I'm receiving the following error ``` WARNING [bioservices.BioDBNet:130]: The URL (https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json) provided cannot be reached. CRITICAL[bioservices.BioDBNet:711]: HTTPSConnectionPool(host='biodbnet-abcc.ncifcrf.gov', port=443): Max retries exceeded with url: /webServices/rest.php/biodbnetRestApi.json?method=getinputs (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED]...

Wildcard not defined in output of Target Rule

3

By default, Snakemake assumes the first rule in a Snakefile is a "target rule". This means it will not have an `output` section, but this plugin assumes all rules will...

**Is your feature request related to a problem? Please describe.** I do not have a particular problem, but I have an enhancement I would like. I would like to allow...

Add `str` as a valid option for the `save` argument in `scanpy.pl.rank_genes_groups`

1

This is a very small pull request to add `str` to the possible arguments for saving a figure from [`scanpy.pl.rank_genes_groups`][rank-genes-groups]. This addition matches other `save=` arguments, such as from [`scanpy.plotting.highly_variable_genes`][highly-variable-genes],...