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Resources review - specify for each module ( #252

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weaglesBio opened this issue Feb 13, 2024 · 6 comments
Open

Resources review - specify for each module ( #252

weaglesBio opened this issue Feb 13, 2024 · 6 comments
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@yumisims @DLBPointon @weaglesBio
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adjust resources Updates to base.config to optimise resources for all data sizes.. enhancement New feature or request

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@weaglesBio
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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.
@weaglesBio weaglesBio added enhancement New feature or request adjust resources Updates to base.config to optimise resources for all data sizes.. labels Feb 13, 2024
@DLBPointon
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DLBPointon commented Feb 13, 2024 •
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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
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UCSC_BEDGRAPHTOBIGWIG = bed.size()

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

@DLBPointon
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Windowmasker needs less resources

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

@DLBPointon DLBPointon mentioned this issue Feb 13, 2024
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@DLBPointon
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Windowmasker needs double the current assignment

@DLBPointon DLBPointon mentioned this issue Feb 15, 2024
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@yumisims yumisims

@DLBPointon DLBPointon

@weaglesBio weaglesBio

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adjust resources Updates to base.config to optimise resources for all data sizes.. enhancement New feature or request
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@yumisims @DLBPointon @weaglesBio