mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-11 04:23:10 +00:00
Merge pull request #335 from jfy133/master
Remove reference to now-decomissioned dracro @ MPCDF & clean up eager @EVA
This commit is contained in:
commit
a412510ce8
3 changed files with 68 additions and 73 deletions
|
@ -42,7 +42,6 @@ profiles {
|
|||
|
||||
singularity {
|
||||
cacheDir = "/mnt/archgen/tools/singularity/containers/"
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -61,110 +61,110 @@ 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 -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: fastqc {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: adapter_removal {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: samtools_flagstat {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
}
|
||||
|
||||
withName: samtools_flagstat_after_filter {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
}
|
||||
|
||||
withName: dedup {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: markduplicates {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
memory = { check_max( 20.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: library_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
}
|
||||
|
||||
withName: seqtype_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
}
|
||||
|
||||
withName: additional_library_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName: metagenomic_complexity_filter {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
}
|
||||
|
||||
withName: malt {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
||||
cpus = { check_max( 32, 'cpus' ) }
|
||||
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName: maltextract {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: multivcfanalyzer {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: mtnucratio {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: vcf2genome {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: qualimap {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
|
||||
}
|
||||
|
||||
withName: damageprofiler {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: circularmapper {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: circulargenerator {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: preseq {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
||||
}
|
||||
|
||||
withName: genotyping_ug {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
|
@ -191,7 +191,7 @@ profiles {
|
|||
maxRetries = 2
|
||||
|
||||
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
||||
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${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" }
|
||||
|
||||
withLabel:'sc_tiny'{
|
||||
cpus = { check_max( 1, 'cpus' ) }
|
||||
|
@ -231,58 +231,58 @@ profiles {
|
|||
// Fixes for SGE and Java incompatibility due to (and also some samtools?!) using more memory than you tell it to use
|
||||
|
||||
withName: makeSeqDict {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: fastqc {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: adapter_removal {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: samtools_flagstat {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
}
|
||||
|
||||
withName: samtools_flagstat_after_filter {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
}
|
||||
|
||||
withName: dedup {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: markduplicates {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: library_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
}
|
||||
|
||||
withName: seqtype_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
}
|
||||
|
||||
withName: additional_library_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName: metagenomic_complexity_filter {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
}
|
||||
|
||||
withName: malt {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
||||
cpus = { check_max( 32, 'cpus' ) }
|
||||
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
|
@ -293,53 +293,53 @@ profiles {
|
|||
}
|
||||
|
||||
withName: maltextract {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: multivcfanalyzer {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: mtnucratio {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: vcf2genome {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: qualimap {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
|
||||
}
|
||||
|
||||
withName: damageprofiler {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: circularmapper {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: circulargenerator {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: genotyping_ug {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: preseq {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
||||
}
|
||||
|
||||
|
@ -365,7 +365,7 @@ profiles {
|
|||
maxRetries = 2
|
||||
|
||||
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
||||
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${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" }
|
||||
|
||||
withLabel:'sc_tiny'{
|
||||
cpus = { check_max( 1, 'cpus' ) }
|
||||
|
@ -405,50 +405,50 @@ 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 -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: fastqc {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: adapter_removal {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: samtools_flagstat {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
}
|
||||
|
||||
withName: samtools_flagstat_after_filter {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
}
|
||||
|
||||
withName: dedup {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: markduplicates {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
memory = { check_max( 48.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: library_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName: seqtype_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
}
|
||||
|
||||
withName: additional_library_merge {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
|
@ -457,64 +457,64 @@ profiles {
|
|||
}
|
||||
|
||||
withName: metagenomic_complexity_filter {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
}
|
||||
|
||||
withName: malt {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
||||
cpus = { check_max( 32, 'cpus' ) }
|
||||
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: maltextract {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: multivcfanalyzer {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: mtnucratio {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: vcf2genome {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: qualimap {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
|
||||
}
|
||||
|
||||
withName: damageprofiler {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: circularmapper {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: circulargenerator {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: genotyping_ug {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: preseq {
|
||||
clusterOptions = { "-S /bin/bash -V -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" }
|
||||
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
||||
}
|
||||
|
||||
|
|
|
@ -23,10 +23,6 @@ Sets the following parameters:
|
|||
- Max. CPUs: 80
|
||||
- Max. walltime: 24.h
|
||||
|
||||
## draco
|
||||
|
||||
:hammer_and_wrench: under testing.
|
||||
|
||||
## raven
|
||||
|
||||
To use: `-profile raven,mpcdf`
|
||||
|
|
Loading…
Reference in a new issue