mag
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nf-core
Assembly and binning of metagenomes
Adding DIAMOND support alongside Kraken2 and Centrifuge to mag pipeline.
This PR enables the possibility to perform co-binning when using the ancient DNA mode. Once merged, it can close #572 ## PR checklist - [x] This comment contains a description...
### Description of the bug I tried to run nf-core/mag with the `test` profile on a new compute cluster and got the following error: ``` -[nf-core/mag] Pipeline completed with errors-...
### Description of feature A major problem we currently have during development is our CI tests are nowhere near comprehensive enough due to the pipeline utilising extremely large database files...
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
### Description of the bug Fails due to the if/else statement around input to SPLIT_FASTA in binning.nf only consideres maxbin2 and/or metabat or both (CONCOCT does not produce 'unbins'). Should...
### Description of feature Expand documentation to include when/why to use nf-core/mag, and potential downstream analyses that can be utilize nf-core/mag outputs. ```[tasklist] ### Tasks - [ ] https://github.com/nf-core/mag/issues/589 -...
### Description of feature Add CoverM to calculate read alignment metrics for contig/bin alignments ```[tasklist] ### Tasks - [ ] Add coverm/contig to nf-core/modules - [ ] Add coverm/genome to...
### Description of feature [dRep](https://github.com/MrOlm/drep) takes a set of genomes, with CheckM data, and dereplicates them to produce a set of non-overlapping genomes at a specified ANI. As this is...
