millironx/nf-configs
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Update hops profile based on requests from pathogen group

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James A. Fellows Yates 2020-07-08 15:22:33 +02:00 committed by GitHub
parent c57a404f18
commit 1af9ce293c
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1 changed files with 6 additions and 7 deletions
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conf/pipeline/eager/shh.config
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@ -73,8 +73,8 @@ profiles {
bwa_index = '/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' fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict' seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
bwaalnn = 0.04 bwaalnn = 0.01
bwaalnl = 32 bwaalnl = 16
run_bam_filtering = true run_bam_filtering = true
bam_discard_unmapped = true bam_discard_unmapped = true
bam_unmapped_type = 'fastq' bam_unmapped_type = 'fastq'
@ -82,11 +82,11 @@ profiles {
metagenomic_tool = 'malt' metagenomic_tool = 'malt'
metagenomic_min_support_reads = 1 metagenomic_min_support_reads = 1
database = '/projects1/malt/databases/indexed/index040/full-bac-full-vir-etal-nov_2017' database = '/projects1/malt/databases/indexed/index040/full-bac-full-vir-etal-nov_2017'
percent_identity = 90 percent_identity = 85
malt_mode = 'BlastN' malt_mode = 'BlastN'
malt_alignment_mode = 'SemiGlobal' malt_alignment_mode = 'SemiGlobal'
malt_top_percent = 1 malt_top_percent = 1
malt_min_support_mode = 'percent' malt_min_support_mode = 'reads'
malt_min_support_percent = 0.01 malt_min_support_percent = 0.01
malt_max_queries = 100 malt_max_queries = 100
malt_memory_mode = 'load' malt_memory_mode = 'load'
@ -99,10 +99,9 @@ profiles {
maltextract_downsamplingoff = false maltextract_downsamplingoff = false
maltextract_duplicateremovaloff = false maltextract_duplicateremovaloff = false
maltextract_matches = false maltextract_matches = false
maltextract_megansummary = false maltextract_megansummary = true
maltextract_percentidentity = 90.0 maltextract_percentidentity = 85.0
maltextract_topalignment = false maltextract_topalignment = false
maltextract_singlestranded = false
} }
} }
pathogen_loose { pathogen_loose {