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Add custom resource configurations for processes #6

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Add custom resource configurations for processes #6

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44 changes: 44 additions & 0 deletions nextflow.config
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all looks good, my only thought is it might make more sense to have these changes in modules.config? This will certainly work though.

Original file line number Diff line number Diff line change
Expand Up @@ -277,3 +277,47 @@ def check_max(obj, type) {
}
}
}

# Custom Resources
process {
withName: "NFCORE_NANOSEQ:NANOSEQ:TRANSFER_READ_TAGS:PYSAM_TRANSFER_READ_TAGS" {
time = 96.h
memory = 80.GB
}
withName: "NFCORE_NANOSEQ:NANOSEQ:SAMTOOLS_VIEW_FASTQ" {
time = 96.h
}
withName: "NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN" {
time = 96.h
cpus = 20
memory = 40.GB
}
withName: "NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT" {
time = 24.h
cpus = { 8 }
memory = { check_max( 12.GB * task.cpus * task.attempt, "memory" ) }
}
withName: "NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV" {
time = 72.h
memory = 60.GB
}
withName: "NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL" {
time = 96.h
memory = 144.GB
}
withName: "NFCORE_NANOSEQ:NANOSEQ:CHOPPER" {
time = 48.h
cpus = 4
memory = { check_max( 80.GB * task.attempt, "memory" ) }
}
withName: "NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED" {
time = 48.h
cpus = { 1 }
memory = { check_max( 150.GB * task.attempt, "memory" ) }
}
withName: "NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG" {
time = 48.h
cpus = { check_max( 8 * task.attempt, "cpus" ) }
memory = { check_max( 40.GB * task.attempt, "memory" ) }
}
}