Christian Brandt

process.executor is not recognized for certain nextflow versions and process orders in the configs

9

## Bug report ### Expected behavior and actual behavior **TLDR: `process.executor = 'google-lifesciences'` is not recognized for certain nextflow versions if its written before another process {} statment**. We have...

Phage prediction tools to include

8

# List of Tools ## Implement? * [VirMiner(Mining, analyzing, and integrating viral signals from metagenomic data)](https://github.com/TingtZHENG/VirMiner/) * [Paper](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0657-y) + [ ] Docker file created * [VirMine (viral sequences from metagenomes)](https://github.com/thatzopoulos/virMine)...

Validate prediction results via nucleotide shuffling

4

# random nucleotide shuffling for error-prone ont reads to improve/validate read hit * @hoelzer can you add some code and/or github ref for the nucleotide shuffling? * it should be...

* singularity build from docker images sometimes fails * we want to take a look at uploading these images to singularity hub

Hi, when doing an API call to the tower (which was previously working with the git repository), we now get this error message: ``` Execution failed: generic::failed_precondition: while running "nf-workflow-36Os6uMuBvpKiR":...

* new version speed things up -> [link](https://www.biorxiv.org/content/10.1101/2021.06.03.446934v2) * prepared a container for 2.1.3 `nanozoo/eggnog-mapper:2.1.3--c399e85` - 2.1.4 is not on bioconda yet

Report "unused reads" back to the user

1

* report back the number of unused reads back to the User. * Should/Could look like this ```` nanopore reads: 500,000 reads used from 2,000,000 Illumina reads: 2500,000 reads used...

update guppy

4

new guppy version 6 does not require arrangement files for demultiplexing and has some changes demulti like this ``` process collect_fastq { label 'demultiplex' input: tuple val(name), val(technology), path(dir) output:...