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nextflow.config
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nextflow.config
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manifest {
mainScript = 'sourmash.nf'
}
profiles {
docker {
executor = 'local'
process.container = 'chancsu/nextflow_sourmash'
docker.enabled = true
}
singularity {
executor = 'local'
process.container = 'chancsu/nextflow_sourmash'
docker.enabled = false
singularity.enabled = true
singularity.autoMounts = true
}
summitHPC {
docker.enabled = false
singularity.enabled = true
singularity.autoMounts = true
executor = 'slurm'
process.container = 'chancsu/nextflow_sourmash'
process.queue = 'shas'
process.module = ['singularity','jdk/1.8.0']
// process.queueSize = 4
process.clusterOptions = '--job-name=nf_sourmash --export=ALL' // --tasks=4 --nodes=1 --ntasks-per-node=4 --qos=long --mail-type=ALL --chdir <launch loc>
process.$adapter_trimming.time = '30m'
process.$adapter_trimming.cpus = 1
process.$adapter_trimming.memory = '1G'
process.$quality_trimming.time = '30m'
process.$quality_trimming.cpus = 1
process.$quality_trimming.memory = '1G'
process.$kmer_trimming.time = '2h'
process.$kmer_trimming.cpus = 1
process.$kmer_trimming.memory = '512G'
process.$kmer_trimming.queue = 'smem'
process.$sourmash_compute.time = '2h'
process.$sourmash_compute.cpus = 1
process.$sourmash_compute.memory = '1G'
process.$sourmash_compare.time = '2h'
process.$sourmash_compare.cpus = 1
process.$sourmash_compare.memory = '1G'
process.$sourmash_plot.time = '2h'
process.$sourmash_plot.cpus = 1
process.$sourmash_plot.memory = '1G'
}
planet {
executor = 'sge'
process.$adapter_trimming.clusterOptions = '-S /bin/bash'
process.$adapter_trimming.time = '30m'
process.$adapter_trimming.cpus = 1
process.$adapter_trimming.memory = '1G'
process.$adapter_trimming.module = 'scythe'
process.$quality_trimming.clusterOptions = '-S /bin/bash'
process.$quality_trimming.time = '30m'
process.$quality_trimming.cpus = 1
process.$quality_trimming.memory = '1G'
process.$quality_trimming.module = 'sickle'
process.$sourmash_compute.clusterOptions = '-S /bin/bash'
process.$sourmash_compute.penv = 'smp'
process.$sourmash_compute.time = '2h'
process.$sourmash_compute.cpus = 1
process.$sourmash_compute.memory = '1G'
process.$sourmash_compute.module = 'sourmash'
process.$sourmash_compare.clusterOptions = '-S /bin/bash'
process.$sourmash_compare.penv = 'smp'
process.$sourmash_compare.time = '2h'
process.$sourmash_compare.cpus = 1
process.$sourmash_compare.memory = '1G'
process.$sourmash_compare.module = 'sourmash'
process.$sourmash_compare.clusterOptions = '-S /bin/bash'
process.$sourmash_plot.penv = 'smp'
process.$sourmash_plot.time = '2h'
process.$sourmash_plot.cpus = 1
process.$sourmash_plot.memory = '1G'
process.$sourmash_plot.module = 'sourmash'
}
}