diff --git a/conf/base.config b/conf/base.config index c6407a77..8916f5fc 100644 --- a/conf/base.config +++ b/conf/base.config @@ -16,56 +16,32 @@ process { } ] - // single cpus - withLabel: max_cpus_1 { - cpus = {check_max('request', RESOURCES.MAX_CPUS_1, 'cpus')} - } - - // 75% cpus - withLabel: max_cpu_75 { - cpus = {check_max('request', RESOURCES.MAX_CPUS_75, 'cpus' )} - } - - // Half cpus - withLabel: max_cpu_50 { - cpus = {check_max('request', RESOURCES.MAX_CPUS_50, 'cpus' )} - } - - // Memory defaults - withLabel: base_mem_4gb { - memory = {check_max(4.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )} - } - - withLabel: base_mem_8gb { - memory = {check_max(8.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )} - } - // Process specific withLabel: 'assemble_genome' { memory = { meta.runtype == 'hybrid' || params.use_unicycler ? check_max((32.GB * task.attempt), RESOURCES.MAX_MEMORY, 'memory') : check_max((8.GB * task.attempt), RESOURCES.MAX_MEMORY, 'memory')} - time = { meta.runtype == 'hybrid' || params.use_unicycler ? check_max( 2.h * task.attempt, (params.max_time).m, 'time' ) : check_max( (params.min_time).m * task.attempt, (params.max_time).m, 'time' )} - } - - withLabel: 'gather_samples' { - maxForks = params.max_downloads - maxRetries = 20 + time = { meta.runtype == 'hybrid' || params.use_unicycler ? check_max( 2.h * task.attempt, (params.max_time).m, 'time' ) : check_max( (params.min_time).m * task.attempt, (params.max_time).m, 'time' )} } // Modules imported from nf-core + withLabel:process_single { + cpus = { check_max('request' , RESOURCES.MAX_CPUS , 'cpus' )} + memory = { check_max(4.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )} + time = { check_max( 1.h * task.attempt, 2.h * task.attempt , 'time' )} + } withLabel: process_low { - cpus = {check_max('request', RESOURCES.MAX_CPUS, 'cpus')} + cpus = {check_max('request' , RESOURCES.MAX_CPUS , 'cpus' )} memory = {check_max(8.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )} - time = {check_max( 2.h * task.attempt, 2.h * task.attempt, 'time' )} + time = {check_max( 2.h * task.attempt, 2.h * task.attempt , 'time' )} } withLabel: process_medium { - cpus = {check_max('request', RESOURCES.MAX_CPUS, 'cpus')} + cpus = {check_max('request' , RESOURCES.MAX_CPUS , 'cpus' )} memory = {check_max(16.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )} - time = {check_max( 12.h * task.attempt, 12.h * task.attempt, 'time' )} + time = {check_max( 12.h * task.attempt, 12.h * task.attempt , 'time' )} } withLabel: process_high { - cpus = {check_max('request', RESOURCES.MAX_CPUS, 'cpus')} + cpus = {check_max('request' , RESOURCES.MAX_CPUS , 'cpus' )} memory = {check_max(64.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )} - time = {check_max( 24.h * task.attempt, 24.h * task.attempt, 'time' )} + time = {check_max( 24.h * task.attempt, 24.h * task.attempt , 'time' )} } withLabel: process_long { time = {check_max( 96.h * task.attempt, 96.h * task.attempt, 'time' )} diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index 3766698b..65b4e73e 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -16,7 +16,7 @@ requirements: - pip - python >3.8 run: - - bactopia-py >=1.0.0 + - bactopia-py >=1.0.1 - conda >=22.11.0 - coreutils - mamba >=1.1.0