millironx
/
nf-configs
mirror of https://github.com/MillironX/nf-configs
1
0
Fork 0
Code Issues Packages Releases Activity

Merge pull request #265 from jfy133/eva-eager-subprofiles

Browse Source 
eva/eager: Try new strategy for SGE and Java incompatibility
kevbrick-patch-1
James A. Fellows Yates 3 years ago committed by GitHub
parent 0c3428f5d1 b0e344846d
commit 5c9896b687
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 222 additions and 10 deletions
Show Stats Download Patch File Download Diff File

232
conf/pipeline/eager/eva.config
Unescape Escape View File

@ -69,7 +69,7 @@ process {
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 5)}G,virtual_free=${(task.memory.toGiga() * 5)}G" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: dedup {
@ -77,11 +77,11 @@ process {
}
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 -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=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: malt {
@ -97,7 +97,7 @@ process {
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: vcf2genome {
@ -105,11 +105,11 @@ process {
}
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 -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: circularmapper {
@ -129,21 +129,98 @@ process {
profiles {
big_data {
medium_data {
params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
config_profile_description = 'nf-core/eager medium-data EVA profile provided by nf-core/configs'
}
executor {
queueSize = 6
queueSize = 8
}
process {
maxRetries = 2
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
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" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 24.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
// 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" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -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" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -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" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -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" }
}
withName:hostremoval_input_fastq {
cpus = { check_max( 1, 'cpus' ) }
@ -151,6 +228,67 @@ profiles {
time = 1440.h
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -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" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -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" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -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" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -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" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -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' }
}
}
}
big_data {
params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
}
executor {
queueSize = 6
}
process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
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" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
@ -192,6 +330,80 @@ profiles {
memory = { check_max( 512.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
// 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" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -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" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -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" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName:hostremoval_input_fastq {
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = 1440.h
}
withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -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" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -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" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -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" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -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" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -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' }
}
}
}

Write Preview
Loading…
Cancel
Save