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sanger-tol / treeval

Pipelines for the production of Treeval data
https://pipelines.tol.sanger.ac.uk/treeval
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Resources review - specify for each module ( #252

Open weaglesBio opened 7 months ago

weaglesBio commented 7 months ago

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 these specifically.

DLBPointon commented 7 months ago

SELFCOMP_SPLITFASTA Single withName: SELFCOMP_MAPIDS|SELFCOMP_MUMMER2BED fasta.size() n Log10(n) n=lines in file - BEDTOOLS_MERGE | BEDTOOLS SORT 30 ref SELFCOMP_ALIGNMENTBLOCKS

DLBPointon commented 7 months ago

UCSC_BEDGRAPHTOBIGWIG = bed.size()

DLBPointon commented 7 months ago

SAMTOOLS_MKDUP=bam.size() / 2 BAMTOBED_SORT = bam.size() FASKTPROF genome 10 TBIX normally reference / 2 SYNTENY minimap2 = 30reference

DLBPointon commented 7 months ago

Windowmasker needs less resources

weaglesBio commented 7 months ago

SELFCOMP: BEDTOOLS_MERGE needs to be removed from base.config as no longer used in subworkflow

DLBPointon commented 7 months ago

Windowmasker needs double the current assignment