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annotate CSP2/nextflow.config @ 25:5c609acba34e

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"planemo upload"
author rliterman
date Tue, 03 Dec 2024 15:56:32 -0500
parents 75070dbe67b1
children 792274118b2e
rev   line source
rliterman@0 1 /*
rliterman@0 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rliterman@0 3 CSP2 Nextflow config file
rliterman@0 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rliterman@0 5 Default config options for all compute environments
rliterman@0 6 ----------------------------------------------------------------------------------------
rliterman@0 7 */
rliterman@0 8
rliterman@0 9 // Enable conda
rliterman@0 10 conda.enabled = true
rliterman@0 11
rliterman@0 12 // Import profile settings
rliterman@0 13 includeConfig "conf/profiles.config"
rliterman@0 14
rliterman@15 15 // CPU/memory settings
rliterman@15 16 process {
rliterman@15 17 withLabel: 'mummerMem' {
rliterman@22 18 cpus = 1
rliterman@24 19 // memory = '4 GB'
rliterman@15 20 }
rliterman@24 21 // withLabel: 'skesaMem' {
rliterman@24 22 // memory = '12 GB'
rliterman@24 23 // }
rliterman@15 24 }
rliterman@15 25
rliterman@0 26 // Global default params
rliterman@0 27 params {
rliterman@0 28
rliterman@0 29 // Setting output directory
rliterman@0 30
rliterman@0 31 // Set name for output folder/file prefixes
rliterman@0 32 out = "CSP2_${new java.util.Date().getTime()}"
rliterman@0 33
rliterman@0 34 // Set output parent directory [Default: CWD; Set this to have all output go to the same parent folder, with unique IDs set by --out]
rliterman@0 35 outroot = ""
rliterman@0 36
rliterman@0 37 // CSP2 can run in the following run-modes:
rliterman@0 38
rliterman@0 39 // assemble: Assemble read data (--reads/--ref_reads) into FASTA via SKESA (ignores --fasta/--ref_fasta/--snpdiffs)
rliterman@0 40 // align: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta), run MUMmer alignment analysis for each query/ref combination (ignores --snpdiffs)
rliterman@0 41 // screen: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta) and/or MUMmer output (.snpdiffs), create a report for raw SNP distances between each query and reference assembly
rliterman@0 42 // snp: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta) and/or MUMmer output (.snpdiffs), generate alignments and pairwise distances for all queries based on each reference dataset
rliterman@0 43
rliterman@0 44 runmode = ""
rliterman@0 45
rliterman@0 46 // Location for isolate sequence data
rliterman@0 47 reads = ""
rliterman@0 48 fasta = ""
rliterman@0 49
rliterman@0 50 // Location for reference sequence data
rliterman@0 51 ref_reads = ""
rliterman@0 52 ref_fasta = ""
rliterman@0 53
rliterman@0 54 // IDs for reference sequences (Comma-separated list)
rliterman@0 55 ref_id = ""
rliterman@0 56
rliterman@0 57 // Location for snpdiffs files
rliterman@0 58 snpdiffs = ""
rliterman@0 59
rliterman@0 60 // Read read_info
rliterman@0 61 readext = "fastq.gz"
rliterman@0 62 forward = "_1.fastq.gz"
rliterman@0 63 reverse = "_2.fastq.gz"
rliterman@0 64
rliterman@0 65 ref_readext = "fastq.gz"
rliterman@0 66 ref_forward = "_1.fastq.gz"
rliterman@0 67 ref_reverse = "_2.fastq.gz"
rliterman@0 68
rliterman@0 69 // Analytical variables
rliterman@0 70
rliterman@0 71 // Only consider queries if the reference genome is covered by at least <min_cov>% [Default: 85]
rliterman@0 72 min_cov = 85
rliterman@0 73
rliterman@0 74 // Only consider SNPs from contig alignments longer than <min_len> bp [Default: 500]
rliterman@0 75 min_len = 500
rliterman@0 76
rliterman@0 77 // Only consider SNPs from contig alignments with <min_iden>% identity [Default: 99]
rliterman@0 78 min_iden = 99
rliterman@0 79
rliterman@0 80 // Remove SNPs that occur within <ref_edge>bp from the end of the reference contig [Default: 150]
rliterman@0 81 ref_edge = 150
rliterman@0 82
rliterman@0 83 // Remove SNPs that occur within <query_edge>bp from the end of the query contig [Default: 150]
rliterman@0 84 query_edge = 150
rliterman@0 85
rliterman@0 86 // SNP density filters: Given density windows provided by dwin, purge windows where more than the allowable window SNPs (wsnps) are found
rliterman@0 87 // Default: 3 max per 1000bp, 2 max per 125bp, 1 max per 15bp, filtered from biggest window to smallest
rliterman@0 88 // Set --dwin 0 to disable density filtering
rliterman@0 89 dwin = "1000,125,15"
rliterman@0 90 wsnps = "3,2,1"
rliterman@0 91
rliterman@0 92 // If running refchooser in snp mode, compare queries to the top X references [Default: 1]
rliterman@0 93 n_ref = 1
rliterman@0 94
rliterman@0 95 // If the assembly file contains the string <trim_name>, remove it from the sample name (e.g. '_contigs_skesa')
rliterman@0 96 trim_name = '""'
rliterman@0 97
rliterman@0 98 // If running SNP pipeline, set the maximum percent of isolates with missing data allowed in the final alignment/distances [Default: 50]
rliterman@0 99 max_missing = 50
rliterman@0 100
rliterman@0 101 // Alternate directory for pybedtools tmp files [Default: "" (system default)]
rliterman@0 102 tmp_dir = ""
rliterman@0 103
rliterman@0 104 // Set IDs for isolates to exclude from analysis (Comma-separated list)
rliterman@0 105 exclude = ""
rliterman@0 106
rliterman@0 107 // By default, do not perform edge-filtered SNP rescuing
rliterman@0 108 rescue = "norescue"
rliterman@0 109
rliterman@0 110 // Help function
rliterman@0 111 help = "nohelp"
rliterman@0 112 h = "nohelp"
rliterman@16 113 }