mag
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nf-core
Assembly and binning of metagenomes
### Description of feature Thank you to bring this amazing tool, which really boosts the efficiency of running the metagenome pipeline! I've been using it for quite a long time...
### Description of feature When running `metaSPAdes` as part of nf-core/mag, the first step is the read correction followed by the actual assembly steps. When using the sensible default resource...
### Description of feature It would be good to evaluate the removal of host reads with Bowtie2 and compare different settings.
### Description of feature When running the pipeline with host removal, I often find a reasonable proportion of the resulting bins still get classified by CAT as the host (in...
Hello, I am trying to understand the inputs to the gtdbtk_summary.nf script. I understand that the script is taking the names of the bins discarded by busco and appending it...
### Description of the bug Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 1. The full error message was: Error...
I'm running mag in my institution's cluster and in the `MAG_DEPTHS_PLOT` step I run into the error `_tkinter.TclError: couldn't connect to display "localhost:11.0"`. For what I've read, I guess that's...
### Description of feature [Filtlong]() and [Nanolyse]() are very time-consuming steps in the process for long-read/hybrid datasets, mainly because neither of them can be multi-threaded. [Chopper]() combines [Nanofilt]() and [Nanolyse]()...
Closes https://github.com/nf-core/mag/issues/501 Proposal table: https://github.com/nf-core/mag/issues/501#issuecomment-2139584648 - [x] test (separate run) - [x] test_single_end - [x] test_alternatives - [ ] test_preassembly_binrefine -> might be problematic due to very slow download of...
### Description of feature Decided I wanted to try and bin my data using Vamb, which isn't in the pipeline yet. Would be a useful feature to be able to...