BethYates

Release 2.0 will contain an `--assembly` parameter which will be used directly by the GENOME_STATISTICS:SUMMARYSEQUENCE process.

After disussing this with the ToL Genome Notes editor they would like to see OMark https://omark.omabrowser.org/ included in the set of tools to evaluate an annotation set

To close this issue: 1. Add a new optional parameter `--annotation_set` which takes in a file path for a directory containing ensembl gene annotation. This directory should have files consistent...

The work in #135 goes most of the way to solving this issue, but the output from the subworkflow is currently two files with lots of information rather than one...

Hi Stephania, thats not something that the pipeline can do directly at the moment although we had been considering how to implement a similar use case where we would run...

> Also found a minor issue in the resulting note that can be addressed in 2.0.1. The collector name should be capitalised in > > ``` > The specimen was...

> Good for me ! > > By the way, minor thing, on the full test, It still says "University **Of** Oxford" even though you've got code to turn `Of`...

Add BUSCO to the annotations statistics subworkflow. To do this you can use the existing nf-core busco module https://nf-co.re/modules/busco/ and run BUSCO in proteins mode. You will need to pass...

We need to pass an argument `-y` to the GFFREAD process to tell it to output protein fasta sequences, to do this you need to add the following to the...

We will need to add a block to base.config to set memory, cpus and time for BUSCOPROTEINS. The meta for the input channel to BUSCOPROTEINS doesn't have a value for...