treeval
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sanger-tol
Pipelines for the production of Treeval data
### 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
Write a yaml validator - Checks structure of yaml - Checks paths lead to expected file types - Checks gene_alignment and synteny fields can be resolved
### 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) ```
### Description of the bug need version sort to avoid "chromosome blocks not continuous" ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information...
### Description of feature Create containers to house the bug-fixed versions of the PretextMap, PretextGraph, and PretextSnapshot. These containers will serve as organised environments where the revised implementations of these...
Would be ideal to use conditionals to run specific subworkflows.
### 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...
### Description of the bug two KMER_READ_COVERAGE:FASTK_FASTK in the module.config, second one overite the first one, so no tmp set. ### Command used and terminal output _No response_ ### Relevant...