Daniel Straub

For changing resource allocations please have a look at https://nf-co.re/mag/2.1.1/usage#resource-requests Meaning, add to your coomand line `-c gtdb.config` where `gtdb.config` contains: ``` process { withName: GTDBTK_DB_PREPARATION { cpus = 12...

> By the way...I was wondering if this error could be repeated in a couple of modules during the pipeline. So, how can I set the parameters adjusting to my...

could it be that the path `/mnt/philippe/Sequenciamento eDNA/Characterizing_lignin-adapted_microbial_communities__eDNA_3rd_pass_30_C_BE-Lig_BY_[eDN3rd30CBELigBY_FD]/Raw_Data/work/f8/c2c7012ccf6d33f184460ac4df19e1/MEGAHIT/tmp/reads.lib` makes problems? I have never seen square brackets, i.e. `[]`, in paths... It might be that MEGAHIT is upset by `Characterizing_lignin-adapted_microbial_communities__eDNA_3rd_pass_30_C_BE-Lig_BY_[eDN3rd30CBELigBY_FD]`? Could...

Yes, the QIIME2 container seems to be broken for docker (which is used for GitHub tests, but it is fine with singularity that I use to test the pipeline locally)....

I close that for now.

Looks good, but I was not able to find (in short time) whether they have some sort of versioning or whether there are several versions or when it was updated...

Great news! Than it might make sense to wait with the benchmarking until that algorithm of your colleagues is here anyway.

And now published properly: https://www.nature.com/articles/s41592-022-01431-4

Totally agree. That would be a major enhancement, also some significant work though. It requires an nanopore-only assemblers, e.g. flye, and mapping processes for contig/mag quantification. If you have favorite...

Oh, there might be a slight misunderstanding: Currently, **there is already the possibility to use Nanopore data**, but only _in addition_ to Illumina data, _not_ on its own (i.e. Nanopore-only)....