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run.config
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executor {
$slurm {
queueSize = 30
}
$local {
cpus = 1
memory = '4 GB'
}
}
process {
executor = "slurm"
cache = "lenient"
//container = "oras://ghcr.io/cschu/nevermore@sha256:b83832ee9a88a8446ef1c6df9b091bb9725a04971b46e454b1d02d12b8d3f064"
maxRetries = 4
errorStrategy = {task.attempt <= 3 ? "retry" : "ignore"}
withName: prepare_fastqs {
executor = "local"
scratch = null
container = null
}
withName: fastqc {
container = "quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
cpus = 2
memory = {4.GB * task.attempt}
time = {4.h * task.attempt}
}
withName: multiqc {
container = "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
publishDir = [ path: params.output_dir, mode: params.publish_mode ]
cpus = 1
memory = {4.GB * task.attempt}
time = {4.h * task.attempt}
}
withName: flagstats {
container = "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
cpus = 2
//memory = {8.GB * task.attempt}
//memory = {bam.size() < 10.GB ? 8.GB * task.attempt : (bam.size() < 30.GB ? 16.GB * task.attempt : 32.GB * task.attempt)}
memory = {2.GB * task.attempt}
time = {4.h * task.attempt}
}
withLabel: kraken2 {
container = "quay.io/biocontainers/kraken2:2.1.3--pl5321hdcf5f25_0"
cpus = 8
memory = {64.GB * task.attempt}
time = '7d'
}
withLabel: bbduk {
container = "quay.io/biocontainers/bbmap:39.06--h92535d8_0"
cpus = 4
memory = {8.GB * task.attempt}
time = '2h'
}
withName: concat_singles {
cpus = 1
memory = '2.GB'
time = '8h'
}
withLabel: align {
container = "quay.io/biocontainers/bwa:0.7.3a--he4a0461_9"
cpus = 8
// 16.GB for IGC, 128.GB for human-gut GMGC
memory = {128.GB * task.attempt}
time = '14d'
}
withLabel: samtools {
container = "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
publishDir = [ path: params.output_dir, mode: params.publish_mode ]
cpus = 8
// 16.GB for IGC, 64.GB for human-gut GMGC
memory = {64.GB * task.attempt}
time = '14d'
}
withName: merge_single_fastqs {
container = "quay.io/biocontainers/bbmap:39.06--h92535d8_0"
cpus = 1
memory = {64.GB * task.attempt}
time = {2.d * task.attempt}
scratch = null
}
withName: collate_stats {
publishDir = [ path: params.output_dir, mode: params.publish_mode ]
}
withLabel: megahit {
publishDir = [mode: "copy", path: params.output_dir]
//container = "vout/megahit"
container = "quay.io/biocontainers/megahit:1.2.9--h43eeafb_4"
scratch = null
cpus = 16
memory = {64.GB * task.attempt}
time = {2.d * task.attempt}
}
withName: bwa_index {
container = "quay.io/biocontainers/bwa:0.7.3a--he4a0461_9"
cpus = 1
memory = {8.GB * task.attempt}
time = {2.d * task.attempt}
scratch = null
}
withName: sortmerna {
//container = "https://depot.galaxyproject.org/singularity/sortmerna%3A4.3.6--h9ee0642_0"
container = "quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0"
cpus = 8
memory = {8.GB * task.attempt}
time = {2.d * task.attempt}
scratch = null
}
}
singularity {
enabled = true
autoMounts = true
}