Damon-Lee Pointon
Damon-Lee Pointon
### 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...
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
Add as we come across them: tidk alans script alans script, expanded to larger section of genomic sequence university group
Local testing for small and large and data set. Standard command: ``` bsub -Is -tty -e error -o out -n 2 -q oversubscribed -M4000 -R'select[mem>4000] rusage[mem=4000] span[hosts=1]' 'nextflow run main.nf...
Work with James to get the output of decon as a viewable track. Output is bed, some work on James' end to get it into a format required for display....