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| @@ -0,0 +1,62 @@ | ||
| process { | ||
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| cpus = { check_max( 2 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 8.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 4.h * task.attempt, 'time' ) } | ||
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| errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } | ||
| maxRetries = 1 | ||
| maxErrors = '-1' | ||
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| // Process-specific resource requirements | ||
| // NOTE - Please try and re-use the labels below as much as possible. | ||
| // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. | ||
| // If possible, it would be nice to keep the same label naming convention when | ||
| // adding in your local modules too. | ||
| // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors | ||
| withLabel:process_single { | ||
| cpus = { check_max( 1 , 'cpus' ) } | ||
| memory = { check_max( 6.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 4.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_very_low { | ||
| cpus = { check_max( 2 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 6.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 3.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_low { | ||
| cpus = { check_max( 4 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 12.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 6.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_medium { | ||
| cpus = { check_max( 8 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 36.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 8.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_high { | ||
| cpus = { check_max( 12 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 72.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 16.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_long { | ||
| time = { check_max( 20.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_high_memory { | ||
| memory = { check_max( 200.GB * task.attempt, 'memory' ) } | ||
| } | ||
| withLabel:error_ignore { | ||
| errorStrategy = 'ignore' | ||
| } | ||
| withLabel:error_retry { | ||
| errorStrategy = 'retry' | ||
| maxRetries = 2 | ||
| } | ||
| } | ||
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| params { | ||
| // Defaults only, expecting to be overwritten | ||
| max_memory = 128.GB | ||
| max_cpus = 16 | ||
| max_time = 240.h | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,90 @@ | ||
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| params { | ||
| chunksize = 1000000 | ||
| output_prefix_file = "psm" | ||
| file_num = 20 | ||
| partitions = "" | ||
| } | ||
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| includeConfig 'conf/base.config' | ||
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| profiles { | ||
| docker { | ||
| docker.enabled = true | ||
| conda.enabled = false | ||
| singularity.enabled = false | ||
| podman.enabled = false | ||
| shifter.enabled = false | ||
| charliecloud.enabled = false | ||
| apptainer.enabled = false | ||
| docker.runOptions = '-u $(id -u):$(id -g)' | ||
| } | ||
| arm { | ||
| docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' | ||
| } | ||
| singularity { | ||
| singularity.enabled = true | ||
| singularity.autoMounts = true | ||
| conda.enabled = false | ||
| docker.enabled = false | ||
| podman.enabled = false | ||
| shifter.enabled = false | ||
| charliecloud.enabled = false | ||
| apptainer.enabled = false | ||
| } | ||
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| ebislurm{ | ||
| conda.enable = false | ||
| docker.enabled = false | ||
| singularity.enabled = true | ||
| executor { | ||
| name = "slurm" | ||
| queueSize = 1000 | ||
| submitRateLimit = "10/1sec" | ||
| exitReadTimeout = "30 min" | ||
| jobName = { | ||
| task.name // [] and " " not allowed in lsf job names | ||
| .replace("[", "(") | ||
| .replace("]", ")") | ||
| .replace(" ", "_") | ||
| } | ||
| } | ||
| singularity.autoMounts = false | ||
| singularity.runOptions = '-B /hps/nobackup/juan/pride/reanalysis:/hps/nobackup/juan/pride/reanalysis' | ||
| singularity.cacheDir = "/hps/nobackup/juan/pride/reanalysis/singularity/" | ||
| } | ||
| } | ||
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| // Function to ensure that resource requirements don't go beyond | ||
| // a maximum limit | ||
| def check_max(obj, type) { | ||
| if (type == 'memory') { | ||
| try { | ||
| if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) | ||
| return params.max_memory as nextflow.util.MemoryUnit | ||
| else | ||
| return obj | ||
| } catch (all) { | ||
| println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" | ||
| return obj | ||
| } | ||
| } else if (type == 'time') { | ||
| try { | ||
| if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) | ||
| return params.max_time as nextflow.util.Duration | ||
| else | ||
| return obj | ||
| } catch (all) { | ||
| println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" | ||
| return obj | ||
| } | ||
| } else if (type == 'cpus') { | ||
| try { | ||
| return Math.min( obj, params.max_cpus as int ) | ||
| } catch (all) { | ||
| println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" | ||
| return obj | ||
| } | ||
| } | ||
| } |