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| params { | ||
| config_profile_name = 'apollo' | ||
| config_profile_description = 'COH Apollo cluster profile provided by nf-core/configs.' | ||
| config_profile_contact = 'Denis O\'Meally (@drejom) or HPRCC Helpdesk ([email protected])' | ||
| config_profile_url = 'https://www.cityofhope.org/ Intranet http://hprcc.coh.org/' | ||
| max_memory = 1500.GB | ||
| max_cpus = 72 | ||
| max_time = 500.h | ||
| igenomes_base = '/ref_genome/igenomes' | ||
| } | ||
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| process { | ||
| executor = 'slurm' | ||
| queue = 'all' | ||
| beforeScript = 'module load singularity' | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| libraryDir = '/opt/singularity-images/nextflow' | ||
| } | ||
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| executor { | ||
| name = 'slurm' | ||
| queueSize = 1000 | ||
| } | ||
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| cleanup = true | ||
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| profiles { | ||
| debug { | ||
| cleanup = false | ||
| } | ||
| } |
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| params { | ||
| config_profile_description = 'Biowulf nf-core config' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://hpc.nih.gov/apps/nextflow.html' | ||
| max_memory = '224 GB' | ||
| max_cpus = 32 | ||
| max_time = '72 h' | ||
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| igenomes_base = '/fdb/igenomes/' | ||
| } | ||
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| executor { | ||
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| $slurm { | ||
| queue = 'norm' | ||
| queueSize = 200 | ||
| pollInterval = '2 min' | ||
| queueStatInterval = '5 min' | ||
| submitRateLimit = '6/1min' | ||
| retry.maxAttempts = 1 | ||
| } | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| cacheDir = "/data/$USER/singularity" | ||
| envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH' | ||
| } | ||
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| env { | ||
| SINGULARITY_CACHEDIR="/data/$USER/singularity" | ||
| PYTHONNOUSERSITE = 1 | ||
| } | ||
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| process { | ||
| executor = 'slurm' | ||
| maxRetries = 1 | ||
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| clusterOptions = ' --gres=lscratch:200 ' | ||
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| scratch = '/lscratch/$SLURM_JOBID' | ||
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| stageInMode = 'symlink' | ||
| stageOutMode = 'rsync' | ||
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| // for running pipeline on group sharing data directory, this can avoid inconsistent files timestamps | ||
| cache = 'lenient' | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,54 +1,55 @@ | ||
| //Profile config names for nf-core/configs | ||
| params { | ||
| config_profile_description = 'Cancer Research UK Manchester Institute HPC cluster profile provided by nf-core/configs' | ||
| config_profile_contact = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)' | ||
| config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki' | ||
| config_profile_contact = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)' | ||
| config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki' | ||
| } | ||
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| singularity { | ||
| cacheDir = '/lmod/nextflow_software' | ||
| enabled = true | ||
| cacheDir = '/lmod/nextflow_software' | ||
| enabled = true | ||
| autoMounts = true | ||
| } | ||
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| process { | ||
| beforeScript = 'module load apps/singularity/3.8.0' | ||
| executor = 'pbs' | ||
| beforeScript = 'module load apps/apptainer/1.2.0' | ||
| executor = 'slurm' | ||
| queue = { task.memory <= 240.GB ? 'compute' : 'hmem' } | ||
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| errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'} | ||
| maxErrors = '-1' | ||
| maxRetries = 3 | ||
| maxErrors = '-1' | ||
| maxRetries = 3 | ||
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| withLabel:process_single { | ||
| cpus = { check_max( 1 * task.attempt, 'cpus' ) } | ||
| cpus = { check_max( 1 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 5.GB * task.attempt, 'memory' ) } | ||
| } | ||
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| withLabel:process_low { | ||
| cpus = { check_max( 1 * task.attempt, 'cpus' ) } | ||
| cpus = { check_max( 1 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 5.GB * task.attempt, 'memory' ) } | ||
| } | ||
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| withLabel:process_medium { | ||
| cpus = { check_max( 4 * task.attempt, 'cpus' ) } | ||
| cpus = { check_max( 4 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 20.GB * task.attempt, 'memory' ) } | ||
| } | ||
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| withLabel:process_high { | ||
| cpus = { check_max( 16 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 80.GB * task.attempt, 'memory' ) } | ||
| cpus = { check_max( 48 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 240.GB * task.attempt, 'memory' ) } | ||
| } | ||
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| } | ||
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| executor { | ||
| name = 'pbs' | ||
| queueSize = 1000 | ||
| name = 'slurm' | ||
| queueSize = 1000 | ||
| pollInterval = '10 sec' | ||
| } | ||
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| params { | ||
| max_memory = 2000.GB | ||
| max_cpus = 32 | ||
| max_time = 72.h | ||
| max_memory = 4000.GB | ||
| max_cpus = 96 | ||
| max_time = 72.h | ||
| } |
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