Christian Brandt

added recommendation from martin: * [FastViromeExplorer](https://github.com/saima-tithi/FastViromeExplorer) also edit: dded FastViromeExplorer "In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages...

we tag the container /tool used with their version number, [see here](https://github.com/replikation/What_the_Phage/blob/master/configs/container.config). However some don't have a version number as pointed out by @mult1fractal

@l-r-den depending on the system WtP tryies to parallel run samples and analyses. but it depends on the process (some need more cpu/ram). you can control this with the max_cores...

ah no the `--no-check-certificate` needs to be added to the `wget` command within the workflow. @mult1fractal can you check and update any wget where its missing?

@mdhishamshaikh could you try a more recent version of WtP? (e.g. v1.1.0) i think @mult1fractal fixed some of the `wget` issues in more recent versions

* what about this: https://github.com/deprekate/PHANOTATE

* thank you very much, this is really helpful * due to our modular coding approach we can easily add these tools to our workflow which is the point/goal of...

hi * iam currently running singularity test runs to reproduce the error * yes the deps are located in an image build from a (working) dockerimage, iam also confused about...

Hi, i was not able to reproduce the error. would you please manually remove the concoct image and retry it? I tested the most recent master from git and let...

hi can you show me the file names. we currently (which is not optimal) have the following regexp to gather the Illumina pairs: `*_R{1,2}.fastq{,.gz}` so I think muffin is not...