Daniel Straub
Daniel Straub
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
I think it would be good to have a module for [trycycler](https://bioconda.github.io/recipes/trycycler/README.html) - [x] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command - [x] There is...
## Is your feature request related to a problem? Please describe I am wondering how our current methods compare in the CAMI II challenge. We should make sure that we...
## Description of the bug With _very_ large metagenomes (here: 122 million contigs), process `NFCORE_MAG:MAG:METABAT2_BINNING:BOWTIE2_ASSEMBLY_BUILD` fails with ``` Command error: WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container...
## Describe the solution you'd like Smoothing out coverage by removing redundant data (very high coverage) might improve assemblies and speed up assembly. Digital normalisation could help here. The pipeline...
Probably it could be interesting to use [Binnacle](https://doi.org/10.3389/fmicb.2021.638561) for scaffolding Megahit contigs to aid binning. However, a quick search on bioconda was not successful and there seems [no release](https://github.com/marbl/binnacle) in...
To save a lot of storage space in the results folder, routinely - ~~compress assembler output:~~ **Done in #67** -- ~~SPAdes: *.fasta, *.gfa~~ -- ~~MEGAHIT: *.fa~~ - compress genome bin...
This updates QIIME2 to the most recent container, Picrust2, and nf-core modules. Hm, tests worked locally, but in CI they fail with: ``` Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT (GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT)' Caused...
### Description of feature This relates to https://github.com/nf-core/ampliseq/issues/368#issuecomment-1041150714 Essentially, it would be nice to use the provided metadata to make relative abundance means across groups and probably immediately barplots with...