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nf-core
Assembly and binning of metagenomes
## Is your feature request related to a problem? Please describe `mag` currently implements taxonomic profiling and metagenome assembly, it would be greatly improved if a functional profile step was...
## Is your feature request related to a problem? Please describe I was using the nf-core/mag pipeline on a bunch of samples recently, and the GTDB-Tk classify workflow step kept...
Add tests using the new parameters `--coassemble_group` and `--binning_map_mode `. Use `strategy.matrix` to parallelise them.
I was trying to run mag with the local instance of Kraken2 database as opposed to compressed minikraken. But from slack discussion learned that mag is configured only to process...
## Is your feature request related to a problem? Please describe At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only). ## Describe the solution you'd like...
## 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...