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windowmasker resource #268

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merged 1 commit into from
Feb 19, 2024
Merged

windowmasker resource #268

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15 changes: 10 additions & 5 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -132,12 +132,11 @@ process {
time = { check_max( 10.h * task.attempt, 'time' ) }
}

// Standard parameters, covers most insecta
// Standard parameters, covers most insecta. However the memory should be approx 10 * genome size
withName: '.*:.*:READ_COVERAGE:MINIMAP2_ALIGN' {
cpus = { check_max( 20 * 1, 'cpus' ) }
memory = { check_max( 50.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * (reference.size() < 1e9 ? 10 : reference.size() < 2.5e9 ? 30 : 300), 'time' ) }
//time = { check_max( 30.h * task.attempt, 'time' ) }
}

withName: '.*:.*:READ_COVERAGE:SAMTOOLS_SORT' {
Expand Down Expand Up @@ -284,17 +283,23 @@ process {
//
withName: '.*:.*:SYNTENY:MINIMAP2_ALIGN' {
cpus = { check_max( 20 * 1, 'cpus' ) }
memory = { check_max( 1.1.GB * Math.ceil( (reference.size() / 1e+9) * 30 ) * task.attempt, 'memory' ) }
memory = { check_max( 1.1.GB * Math.ceil( (reference.size() / 1e+9) * 30 ) * task.attempt, 'memory' ) }
time = { check_max( 20.h * task.attempt, 'time' ) }
}

//
// SUBWORKFLOW: REPEAT_DENSITY
//

withName: '(WINDOWMASKER_MKCOUNTS|WINDOWMASKER_USTAT)' {
withName: WINDOWMASKER_MKCOUNTS {
cpus = { check_max( 6 , 'cpus' ) }
memory = { check_max( 1.5.GB * Math.ceil( ref.size() / 1e+9 ) * task.attempt, 'memory' ) }
time = { check_max( 10.h * task.attempt , 'time' ) }
}

withName: WINDOWMASKER_USTAT {
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 5.GB * task.attempt , 'memory' ) }
memory = { check_max( 1.GB * Math.ceil( ref.size() / 2e+9 ) * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt , 'time' ) }
}
}
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