/* section below needs to be adjusted to local cluster */

profiles {

	embl_hpc {
 		process.executor = 'slurm'
		process.queueSize = 300
		process.queue = 'htc-el8'
		process.clusterOptions = "-A zeller"
	}

	harvard {
		process.executor = 'lsf'
		process.queueSize = 300
		process.queue = ''
		process.clusterOptions = ''
	}

}


process {
	cache = "lenient"
	container = "oras://ghcr.io/cschu/vortex_knight@sha256:f01a08ba83c59e9ddb5ce69c2f3bd2179e13122e631f4836444699a9f064dd8d"
	withName: fastqc {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 2
		memory = {4.GB * task.attempt}
		time = '7d'
		maxRetries = 3
	}
	withName: multiqc {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 1
		memory = {4.GB * task.attempt}
		time = '7d'
		maxRetries = 3
	}
	withName: fq2fa {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 1
		memory = {8.GB * task.attempt}
		time = {2.h * task.attempt}
		maxRetries = 3
	}
	withName: bam2fq {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 8
		memory = {bam.size() < 10.GB ? 8.GB * task.attempt : (bam.size() < 30.GB ? 16.GB * task.attempt : 32.GB * task.attempt)}
		time = '7d'
		maxRetries = 3
	}
	withName: fq2bam {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 2
		memory = {32.GB * task.attempt}
		time = '7d'
		maxRetries = 3
	}
	withName: flagstats {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 2
		memory = {2.GB * task.attempt}
		time = '7d'
		maxRetries = 3
	}
	withName: remove_host_kraken2 {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 8
		memory = {64.GB * task.attempt}
		time = '7d'
		maxRetries = 3
	}
	withLabel: kraken2 {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 8
		memory = {64.GB * task.attempt}
		time = '7d'
		maxRetries = 3
	}
	withName: pathseq {
		errorStrategy = {task.attempt <= 8 ? "retry" : "ignore"}
		cpus = 1
		memory = {256.GB * task.attempt}
		time = '7d'
		maxRetries = 8
	}
	withLabel: bbduk {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 4
		memory = {8.GB * task.attempt}
		time = '2h'
		maxRetries = 3
	}
	withName: qc_bbmerge {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 4
		memory = {16.GB * task.attempt}
		time = '2h'
		maxRetries = 3
	}
	withName: concat_singles {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 1
		memory = '2.GB'
		time = '8h'
		maxRetries = 3
	}
	withName: collate_results {
		errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
		cpus = 1
		memory = {16.GB * task.attempt}
		time = {8.h * task.attempt}
		maxRetries = 3
	}
}

singularity {
	enabled = true
	autoMounts = true
}