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221 lines
6.8 KiB
Plaintext
221 lines
6.8 KiB
Plaintext
// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
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igenomes_base = "/projects1/public_data/igenomes/"
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}
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// Specific nf-core/eager process configuration
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process {
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maxRetries = 3
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withName: malt {
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maxRetries = 1
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memory = { task.attempt > 1 ? 1900.GB : 725.GB }
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cpus = { task.attempt > 1 ? 112 : 64 }
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time = 1440.h
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queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
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}
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withName: circulargenerator {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'sc_small'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'sc_medium'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_small'{
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cpus = { check_max( 2, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_medium' {
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cpus = { check_max( 4, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_large'{
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cpus = { check_max( 8, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_huge'{
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cpus = { check_max( 32, 'cpus' ) }
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memory = { check_max( 256.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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}
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profiles {
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big_data {
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager big-data SHH profile provided by nf-core/configs'
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}
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executor {
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queueSize = 6
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}
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process {
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maxRetries = 2
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withName:malt {
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maxRetries = 1
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memory = { task.attempt > 1 ? 1900.GB : 725.GB }
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cpus = { task.attempt > 1 ? 112 : 64 }
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time = 1440.h
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queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
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}
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withName:hostremoval_input_fastq {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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time = 1440.h
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queue = 'long'
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}
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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withLabel:'sc_small'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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withLabel:'sc_medium'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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withLabel:'mc_small'{
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cpus = { check_max( 2, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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withLabel:'mc_medium' {
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cpus = { check_max( 4, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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withLabel:'mc_large'{
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cpus = { check_max( 8, 'cpus' ) }
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memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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withLabel:'mc_huge'{
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cpus = { check_max( 32, 'cpus' ) }
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memory = { check_max( 512.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : 48.h }
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}
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}
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}
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microbiome_screening {
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process {
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// Assuming NCBI NT-sized DB
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withName: malt {
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maxRetries = 1
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memory = 1900.GB
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cpus = 112
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time = 1440.h
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queue = 'supercruncher'
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}
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}
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}
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// IMPORTANT this profile is not reproducible due to hardcoded paths. For initial/automated screening ONLY.
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hops {
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params {
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config_profile_description = 'Rough HOPS screening MPI-SHH profile, provided by nf-core/configs.'
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fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
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bwa_index = '/projects1/Reference_Genomes/Human/HG19/'
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fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
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seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
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bwaalnn = 0.01
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bwaalnl = 16
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run_bam_filtering = true
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bam_unmapped_type = 'fastq'
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run_metagenomic_screening = true
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metagenomic_tool = 'malt'
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metagenomic_min_support_reads = 1
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database = '/projects1/malt/databases/indexed/index040/full-bac-full-vir-etal-nov_2017'
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percent_identity = 85
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malt_mode = 'BlastN'
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malt_alignment_mode = 'SemiGlobal'
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malt_top_percent = 1
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malt_min_support_mode = 'reads'
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malt_max_queries = 100
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malt_memory_mode = 'load'
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run_maltextract = true
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maltextract_taxon_list = '/projects1/users/key/anc5h/soi.backup/List_of_pathogens_KB_fmk12_wViruses1.txt'
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maltextract_ncbifiles = '/projects1/clusterhomes/huebler/RMASifter/RMA_Extractor_Resources/'
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maltextract_filter = 'def_anc'
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maltextract_toppercent = 0.01
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maltextract_destackingoff = false
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maltextract_downsamplingoff = false
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maltextract_duplicateremovaloff = false
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maltextract_matches = false
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maltextract_megansummary = true
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maltextract_percentidentity = 85.0
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maltextract_topalignment = false
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}
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}
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pathogen_loose {
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params {
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config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'
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bwaalnn = 0.01
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bwaalnl = 16
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}
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}
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pathogen_strict {
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params {
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config_profile_description = 'Pathogen (strict) MPI-SHH SDAG profile, provided by nf-core/configs.'
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bwaalnn = 0.1
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bwaalnl = 32
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}
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}
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human {
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params {
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config_profile_description = 'Human MPI-SHH SDAG profile, provided by nf-core/configs.'
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bwaalnn = 0.01
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bwaalnl = 16500
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}
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}
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}
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