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Update hops profile based on requests from pathogen group
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1 changed files with 6 additions and 7 deletions
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@ -73,8 +73,8 @@ profiles {
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bwa_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
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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 = 0.04
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bwaalnl = 32
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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_discard_unmapped = true
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bam_unmapped_type = 'fastq'
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@ -82,11 +82,11 @@ profiles {
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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 = 90
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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 = 'percent'
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malt_min_support_mode = 'reads'
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malt_min_support_percent = 0.01
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malt_max_queries = 100
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malt_memory_mode = 'load'
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@ -99,10 +99,9 @@ profiles {
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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 = false
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maltextract_percentidentity = 90.0
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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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maltextract_singlestranded = false
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}
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}
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pathogen_loose {
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