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nextflow.config
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nextflow.config
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singularity {
enabled = true
autoMounts = true
cacheDir = "/hps/nobackup/rdf/metagenomics/service-team/singularity-cache/"
}
profiles {
standard {
includeConfig 'configs/local.config'
}
slurm {
includeConfig "configs/slurm.config"
process.executor = "slurm"
}
}
params {
outdir = "/hps/nobackup/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_v6"
dummy_fasta = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/dummy.fasta"
empty_file = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/EMPTY.txt"
pipeline_version = "6"
silva_version = "138.1"
silva_download_taxdump = "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2024-01-01.zip"
silva_ssu_label = "SILVA-SSU"
silva_ssu_download_fasta = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/SILVA_${silva_version}_SSURef_tax_silva_trunc.fasta.gz"
silva_ssu_download_taxmap = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/taxmap_slv_ssu_ref_${silva_version}.txt.gz"
silva_lsu_label = "SILVA-LSU"
silva_lsu_download_fasta = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/SILVA_${silva_version}_LSURef_tax_silva_trunc.fasta.gz"
silva_lsu_download_taxmap = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/taxmap_slv_lsu_ref_${silva_version}.txt.gz"
pr2_version = "5.0.0"
pr2_label = "PR2"
pr2_download_fasta = "https://github.com/pr2database/pr2database/releases/download/v${pr2_version}/pr2_version_${pr2_version}_SSU_mothur.fasta.gz"
pr2_download_tax = "https://github.com/pr2database/pr2database/releases/download/v${pr2_version}/pr2_version_${pr2_version}_SSU_mothur.tax.gz"
pr2_tax_header = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/pr2_tax_header.txt"
unite_version = "9.0"
unite_label = "UNITE"
unite_repo_url = "https://doi.plutof.ut.ee/doi/10.15156/BIO/2483926"
unite_download_fasta = "https://files.plutof.ut.ee/public/orig/1A/C1/1AC1288ECCCC67B566050AEEF93A8CC298337B408A24C3E49E17ED28A33AE1BB.gz"
unite_tax_header = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/unite_tax_header.txt"
rfam_version = "14.10"
rfam_label = "RFAM"
rfam_claninfo = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/temp_ribo.claninfo"
rfam_download_cm = "https://ftp.ebi.ac.uk/pub/databases/Rfam/${rfam_version}/Rfam.cm.gz"
itsonedb_version = "1.141"
itsonedb_label = "ITSone"
itsonedb_download_fasta = "https://itsonedb.cloud.ba.infn.it/ExportController?dbexport=ENA"
itsonedb_download_taxdump = "https://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/sdwca.zip"
itsonedb_tax_header = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/itsonedb_tax_header.txt"
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}