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Add a HOPS profile for nf-core/eager @ SHH

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James A. Fellows Yates 2020-07-07 14:31:11 +02:00 committed by GitHub
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1 changed files with 38 additions and 4 deletions
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42
conf/pipeline/eager/shh.config
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@ -5,10 +5,6 @@ params {
config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs' config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
igenomes_base = "/projects1/public_data/igenomes/" igenomes_base = "/projects1/public_data/igenomes/"
// default BWA
bwaalnn = 0.04
bwaalnl = 32
} }
// Specific nf-core/eager process configuration // Specific nf-core/eager process configuration
@ -26,6 +22,44 @@ process {
} }
profiles { profiles {
hops {
pathogen_screening {
fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
bwa_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
bwaalnn = 0.04
bwaalnl = 32
run_bam_filtering = true
bam_discard_unmapped = true
bam_unmapped_type = 'fastq'
run_metagenomic_screening = true
metagenomic_tool = 'malt'
metagenomic_min_support_reads = 1
database = '/projects1/malt/databases/indexed/index040/full-bac-full-vir-etal-nov_2017'
percent_identity = 90
malt_mode = 'BlastN'
malt_alignment_mode = 'SemiGlobal'
malt_top_percent = 1
malt_min_support_mode = 'percent'
malt_min_support_percent = 0.01
malt_max_queries = 100
malt_memory_mode = 'load'
run_maltextract = true
maltextract_taxon_list = '/projects1/users/key/anc5h/soi.backup/List_of_pathogens_KB_fmk12_wViruses1.txt'
maltextract_ncbifiles = '/projects1/clusterhomes/huebler/RMASifter/RMA_Extractor_Resources/'
maltextract_filter = 'def_anc'
maltextract_toppercent = 0.01
maltextract_destackingoff = false
maltextract_downsamplingoff = false
maltextract_duplicateremovaloff = false
maltextract_matches = false
maltextract_megansummary = false
maltextract_percentidentity = 90.0
maltextract_topalignment = false
maltextract_singlestranded = false
}
}
pathogen_loose { pathogen_loose {
params { params {
config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.' config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'