Jim Downie

BUSCO creates a huge number of files - add a flag to remove some of these?

4

### Description of feature Somewhere between a bug and a feature request - I'm running the pipeline and have generated 608 bins. I'm now at the BUSCO step and the...

Genome taxnomic classification with Sourmash

3

### Description of feature I was reading the SourMash documentation, and noticed it can be used for genome classification. Could be a nice one to have - there are pre-made...

CAT_DB_GENERATE issues

3

### Description of the bug CAT_DB_GENERATE fails on my system due to what seem to be network connection issues, despite nodes having internet access: ``` WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]:...

Make all pipeline steps opt-in

11

### Description of feature At the moment, a default pipeline run entails a highly fully-featured run with many optional steps enabled that may or may not be desirable - for...

### Description of feature BUSCO has a batch mode, where the input to the BUSCO call is a directory of fasta files rather than an individual file. As binning can...

Host removal on assembly contigs

1

### 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...

"Population must be a sequence. For dicts or sets, use sorted(d). in line 83" [Python 3.11 compatibility?]

4

Trying to run CAMISIM to generate a very small test metagenome data set with a mixture of eukaryotic and prokaryotic genomes to test a pipeline with, following the example in...

Cannot supply list of matrices to populate 3 dimensional array int

2

**Describe the bug** When trying to supply a list of matrices to an array[x, y, z] int, I get the following error: ``` “Error in mde(x) : ‘list’ object cannot...

Tiara lacks an option to spit out its version number when requested. It would be useful to have this to track the version automatically when writing e.g. a Nextflow pipeline.

Feature request: function for splitting / unflattening lists

1

{purrr} provides `list_flatten()`, which takes a list and removes a single layer of hierarchy. However, it would be quite useful to be able to do the reverse, and "unflatten" a...