Damon-Lee Pointon

Adding nf-test tests and files Adding the option to also include a fai file. If this is not provided then pretext will generate one automatically. Closes #5123

### Is your feature request related to a problem? Please describe PretextMap will index the incoming fasta file, in many cases this file will already be generated and just needs...

## Is your feature request related to a problem? Please describe I am running GitPod as an educational tool, and requesting new members join means they join the organisation as...

[1.2.0] - PacBio Only

5

### Description of feature There has been a request for a PacBio only run. This is something not currently supported, however, should be simple enough to implement. Related to #115

YAML validator

1

Write a yaml validator - Checks structure of yaml - Checks paths lead to expected file types - Checks gene_alignment and synteny fields can be resolved

v2 - PNG display plugin for JBrowse

1

### Description of feature Curators have developed some scripts to generate images which cover the whole genome. Would be good if these can be run on request and displayed if...

### Description of feature Issue brought up by TreeValGal paper - rightfully so in this case ``` bin/juicer_tools.1.8.9_jcuda.0.8.jar: Java archive data (JAR) bin/telomere.jar: Java archive data (JAR) ```

Flags to run X subworkflow

1

Would be ideal to use conditionals to run specific subworkflows.

[1.2.0 - Ancient Destiny] Chunk fasta reads for better parallelization for revio pacbio data

4

### Description of feature The size of the revio data is huge, this needs to be split into n = (reads / 10million) files. Mapping and then merge the output.

### Description of feature I've updated most of our NF-Core modules to the new NF-Test standard, about ~18 so far, so I need to do another round of module updates...