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Merge pull request #269 from jfy133/eva-eager-subprofiles

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More Java overhead fixes and update container cache location for eager @EVA
This commit is contained in:
James A. Fellows Yates 2021-09-06 15:00:22 +02:00 committed by GitHub
commit 4087ca13dd
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2 changed files with 89 additions and 59 deletions
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2
conf/eva.config
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@ -39,7 +39,7 @@ profiles {
}
singularity {
cacheDir = "/mnt/archgen/users/singularity_scratch"
cacheDir = "/mnt/archgen/tools/singularity/containers/"
}

146
conf/pipeline/eager/eva.config
View file

@ -14,7 +14,7 @@ process {
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -61,72 +61,82 @@ process {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: seqtype_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: additional_library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
}
@ -152,7 +162,7 @@ profiles {
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -199,32 +209,42 @@ profiles {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: seqtype_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: additional_library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
}
withName:hostremoval_input_fastq {
cpus = { check_max( 1, 'cpus' ) }
@ -233,43 +253,43 @@ profiles {
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
@ -295,7 +315,7 @@ profiles {
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -342,28 +362,36 @@ profiles {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: seqtype_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: additional_library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName:hostremoval_input_fastq {
cpus = { check_max( 1, 'cpus' ) }
@ -372,47 +400,49 @@ profiles {
}
withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}