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nextflow.ica.config
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nextflow.ica.config
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if(params.ica_smoke_test) {
params.input = null
includeConfig 'conf/test.config'
}
params.mode = "PHOENIX"
params.input = null
params.kraken2db = null
params.busco_db_path = null
params.coverage = 30
params.indir = null
params.scaffolds_ext = '.scaffolds.fa.gz'
params.minlength = 500
params.phred = 33
params.input_sra = null
params.use_sra = false
params.microbe_example = "${baseDir}/assets/Microbe.1.0_Example_Data.xlsx"
params.sra_metadata = "${baseDir}/assets/SRA_metadata_example.xlsx"
params.osii_bioprojects = "${baseDir}/assets/osii-bioprojects.yaml"
params.create_ncbi_sheet = false
params.terra = false
params.ica = true
params.placeholder = "${baseDir}/assets/placeholder.txt"
params.bbdukdb = "${baseDir}/assets/databases/phiX.fasta"
params.zipped_sketch = "${baseDir}/assets/databases/REFSEQ_20240124_Bacteria_complete.msh.gz"
params.amrfinder_db = "${baseDir}/assets/databases/amrfinderdb_v3.11_20231115.1.tar.gz"
params.ncbi_assembly_stats = "${baseDir}/assets/databases/NCBI_Assembly_stats_20240124.txt"
params.taxa = "${baseDir}/assets/databases/taxes_20230516.csv"
params.ardb = "${baseDir}/assets/databases/ResGANNCBI_20240131_srst2.fasta"
params.gamdbpf = "${baseDir}/assets/databases/PF-Replicons_20240124.fasta"
params.hvgamdb = "${baseDir}/assets/databases/HyperVirulence_20220414.fasta"
params.custom_mlstdb = "${baseDir}/assets/databases/mlst_db_20240124.tar.gz"
params.nodes = "${baseDir}/assets/databases/nodes_20240129.dmp.gz"
params.names = "${baseDir}/assets/databases/names_20240129.dmp.gz"
params.busco_config = "${baseDir}/conf/modules.config"
params.multiqc_config = null
params.multiqc_title = null
params.max_multiqc_email_size = '25.MB'
params.plaintext_email = false
params.monochrome_logs = false
params.help = false
params.validate_params = true
params.show_hidden_params = false
params.schema_ignore_params = 'ica,nodes,names,sra_metadata,osii_bioprojects,microbe_example,custom_mlstdb,scaffolds_ext,input_sra,amrfinder_db,sra_fastqs,results,placeholder,zipped_sketch,terra,fasta,minlength,phred,ardb,hvgamdb,gamdbpf,taxa,ncbi_assembly_stats,refseq_fasta_database,bbdukdb,path2db,busco_config'
params.custom_config_version = 'master'
params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
params.config_profile_description = null
params.config_profile_contact = null
params.config_profile_url = null
params.config_profile_name = null
params.max_memory = '128.GB'
params.max_cpus = 16
params.max_time = '240.h'
docker.enabled = true
docker.userEmulation = true
params.outdir = 'out'
params.publish_dir_mode = 'copy'
params.conda_enabled = false
params.igenomes_ignore = false
params.enable_conda = false
params.email_on_fail = null
params.email = null
process = [:]
params.ica_smoke_test = false
includeConfig 'conf/base.ica.config'
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
includeConfig 'conf/modules.config'
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}