// Profile config names for nf-core/configs params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs' } // Specific nf-core/eager process configuration process { beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion clusterOptions = { "-l h=!bionode08.eva.mpg.de -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' ) } memory = { check_max( 1.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( 4.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( 8.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( 4.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( 8.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( 16.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 = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: fastqc { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: adapter_removal { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: dedup { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: markduplicates { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: library_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: seqtype_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: additional_library_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: malt { clusterOptions = { "-l h=!bionode08.eva.mpg.de -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 = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: multivcfanalyzer { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: mtnucratio { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: vcf2genome { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: qualimap { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: damageprofiler { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: circularmapper { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: circulargenerator { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: preseq { clusterOptions = { "-l h=!bionode08.eva.mpg.de -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 = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } } profiles { medium_data { params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_description = 'nf-core/eager medium-data EVA profile provided by nf-core/configs' } executor { queueSize = 8 } process { beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion clusterOptions = { "-l h=!bionode08.eva.mpg.de -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' ) } 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 = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: fastqc { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: adapter_removal { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: dedup { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: markduplicates { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: library_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: seqtype_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: additional_library_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: malt { clusterOptions = { "-l h=!bionode08.eva.mpg.de -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 { memory = { check_max( 32.GB * task.attempt, 'memory' ) } time = 1440.h } withName: maltextract { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: multivcfanalyzer { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: mtnucratio { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: vcf2genome { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: qualimap { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: damageprofiler { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: circularmapper { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: circulargenerator { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: genotyping_ug { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: preseq { clusterOptions = { "-l h=!bionode08.eva.mpg.de -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' } } } } 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"' maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion clusterOptions = { "-l h=!bionode08.eva.mpg.de -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' ) } memory = { check_max( 2.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( 8.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( 16.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( 8.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( 16.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( 32.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( 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 = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: fastqc { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: adapter_removal { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: dedup { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: markduplicates { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: library_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } } withName: seqtype_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: additional_library_merge { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } } withName:hostremoval_input_fastq { memory = { check_max( 32.GB * task.attempt, 'memory' ) } time = 1440.h } withName: malt { clusterOptions = { "-l h=!bionode08.eva.mpg.de -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 = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: multivcfanalyzer { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: mtnucratio { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: vcf2genome { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: qualimap { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: damageprofiler { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: circularmapper { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: circulargenerator { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: genotyping_ug { clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: preseq { clusterOptions = { "-l h=!bionode08.eva.mpg.de -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' } } } } pathogen_loose { params { config_profile_description = 'Pathogen (loose) MPI-EVA profile, provided by nf-core/configs.' bwaalnn = 0.01 bwaalnl = 16 } } pathogen_strict { params { config_profile_description = 'Pathogen (strict) MPI-EVA SDAG profile, provided by nf-core/configs.' bwaalnn = 0.1 bwaalnl = 32 } } human { params { config_profile_description = 'Human MPI-EVA SDAG profile, provided by nf-core/configs.' bwaalnn = 0.01 bwaalnl = 16500 } } }