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fine tuning
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y-popov committed Mar 11, 2024
1 parent a63f0c6 commit 85f83f0
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Showing 3 changed files with 31 additions and 11 deletions.
36 changes: 28 additions & 8 deletions conf/hgi.config
Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,12 @@ process {

withName: 'GATK4_GENOMICSDBIMPORT' {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
}

withName: 'GATK4_GENOTYPEGVCFS' {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
ext.args = { "-G StandardAnnotation -G AS_StandardAnnotation" }
}

Expand All @@ -30,16 +30,32 @@ process {

withName: 'GATK4_HAPLOTYPECALLER' {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
ext.args = { params.joint_germline ? "-ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation" : "" }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
}

withName: 'MERGE_HAPLOTYPECALLER' {
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
}

withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT' {
memory = { check_max( 256.MB * task.attempt, 'memory' ) }
}

withName: 'VARIANTRECALIBRATOR_INDEL' {
ext.args = "-AS -an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL"
withName: 'BCFTOOLS_STATS' {
memory = { check_max( 128.MB * task.attempt, 'memory' ) }
}

withName: 'VARIANTRECALIBRATOR_SNP' {
ext.args = "-AS -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
withName: 'VCFTOOLS_TSTV_COUNT|VCFTOOLS_TSTV_QUAL|VCFTOOLS_SUMMARY' {
memory = { check_max( 128.MB * task.attempt, 'memory' ) }
}

withName: CUSTOM_DUMPSOFTWAREVERSIONS {
memory = { check_max( 128.MB * task.attempt, 'memory' ) }
}

withName: 'MULTIQC' {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
}
}

Expand All @@ -48,3 +64,7 @@ singularity {
enabled = true
cacheDir = '/nfs/hgi/singularityContainers/'
}

executor {
queueSize = 4000
}
2 changes: 1 addition & 1 deletion conf/modules/haplotypecaller.config
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
process {

withName: 'GATK4_HAPLOTYPECALLER' {
ext.args = { params.joint_germline ? "-ERC GVCF" : "" }
ext.args = { params.joint_germline ? "-ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation" : "" }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
ext.when = { params.tools && params.tools.split(',').any{ it.startsWith('haplotypecaller') } }
publishDir = [
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4 changes: 2 additions & 2 deletions conf/modules/joint_germline.config
Original file line number Diff line number Diff line change
Expand Up @@ -51,15 +51,15 @@ process {

withName: 'VARIANTRECALIBRATOR_INDEL' {
ext.prefix = { "${meta.id}_INDEL" }
ext.args = "-an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL"
ext.args = "-AS -an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL"
publishDir = [
enabled: false
]
}

withName: 'VARIANTRECALIBRATOR_SNP' {
ext.prefix = { "${meta.id}_SNP" }
ext.args = "-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
ext.args = "-AS -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
publishDir = [
enabled: false
]
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