treeval
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sanger-tol
Pipelines for the production of Treeval data
### Description of feature We should avoid using the defaults (process_low, process_high etc). This is as we know the resource requirements of the processes, so should be able to provide...
### Description of feature The Galaxy_dev is ready to test using the following four samples. (1) iqMecThal1 data type: hic-arima2 and hifi /lustre/scratch124/tol/projects/darwin/data/insects/Meconema_thalassinum/genomic_data/iqMecThal1 (2) aBomBom1 data type: arima2 and clr...
### Description of feature We should have a look at combined runs where the we map for the combined and the split out based on the hap.
### Description of feature .
### Description of the bug CAT_CAT runs everytime it is used, however, alot of the time the grab file process is only finding 1 file. In these cases CAT_CAT should...
### Description of feature Currently testing TreeVal by running daSamNigr - the European elder. The peptide subworkflow, is obviously slower however does not **require** any futher optimizations. GAP_FINDER also requires...
### Description of the bug A large number of the gene set annotations used on treeval are using the ENS number rather than the more desired gene name. This would...
### Description of feature In order to standard coverage and logged coverage, add a track which has hard upper bound. (e.g. max of 5 times the median).
Pyfasta (written in 2018) is archived, it's successor Pyfaidx isn't suitable for our use (no split function). However, there is pyfastx (https://github.com/lmdu/pyfastx) which uses samtools index to do the job...
In sanger we are producing csv putative contamination files. We can convert these to bed for upload as a bed file