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annotate CSP2/nextflow.config @ 0:01431fa12065

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"planemo upload"
author rliterman
date Mon, 02 Dec 2024 10:40:55 -0500
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children 0d775868ee62
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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@0 15 // Global default params
rliterman@0 16 params {
rliterman@0 17
rliterman@0 18 // Setting output directory
rliterman@0 19
rliterman@0 20 // Set name for output folder/file prefixes
rliterman@0 21 out = "CSP2_${new java.util.Date().getTime()}"
rliterman@0 22
rliterman@0 23 // 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 24 outroot = ""
rliterman@0 25
rliterman@0 26 // CSP2 can run in the following run-modes:
rliterman@0 27
rliterman@0 28 // assemble: Assemble read data (--reads/--ref_reads) into FASTA via SKESA (ignores --fasta/--ref_fasta/--snpdiffs)
rliterman@0 29 // 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 30 // 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 31 // 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 32
rliterman@0 33 runmode = ""
rliterman@0 34
rliterman@0 35 // Location for isolate sequence data
rliterman@0 36 reads = ""
rliterman@0 37 fasta = ""
rliterman@0 38
rliterman@0 39 // Location for reference sequence data
rliterman@0 40 ref_reads = ""
rliterman@0 41 ref_fasta = ""
rliterman@0 42
rliterman@0 43 // IDs for reference sequences (Comma-separated list)
rliterman@0 44 ref_id = ""
rliterman@0 45
rliterman@0 46 // Location for snpdiffs files
rliterman@0 47 snpdiffs = ""
rliterman@0 48
rliterman@0 49 // Read read_info
rliterman@0 50 readext = "fastq.gz"
rliterman@0 51 forward = "_1.fastq.gz"
rliterman@0 52 reverse = "_2.fastq.gz"
rliterman@0 53
rliterman@0 54 ref_readext = "fastq.gz"
rliterman@0 55 ref_forward = "_1.fastq.gz"
rliterman@0 56 ref_reverse = "_2.fastq.gz"
rliterman@0 57
rliterman@0 58 // Analytical variables
rliterman@0 59
rliterman@0 60 // Only consider queries if the reference genome is covered by at least <min_cov>% [Default: 85]
rliterman@0 61 min_cov = 85
rliterman@0 62
rliterman@0 63 // Only consider SNPs from contig alignments longer than <min_len> bp [Default: 500]
rliterman@0 64 min_len = 500
rliterman@0 65
rliterman@0 66 // Only consider SNPs from contig alignments with <min_iden>% identity [Default: 99]
rliterman@0 67 min_iden = 99
rliterman@0 68
rliterman@0 69 // Remove SNPs that occur within <ref_edge>bp from the end of the reference contig [Default: 150]
rliterman@0 70 ref_edge = 150
rliterman@0 71
rliterman@0 72 // Remove SNPs that occur within <query_edge>bp from the end of the query contig [Default: 150]
rliterman@0 73 query_edge = 150
rliterman@0 74
rliterman@0 75 // SNP density filters: Given density windows provided by dwin, purge windows where more than the allowable window SNPs (wsnps) are found
rliterman@0 76 // Default: 3 max per 1000bp, 2 max per 125bp, 1 max per 15bp, filtered from biggest window to smallest
rliterman@0 77 // Set --dwin 0 to disable density filtering
rliterman@0 78 dwin = "1000,125,15"
rliterman@0 79 wsnps = "3,2,1"
rliterman@0 80
rliterman@0 81 // If running refchooser in snp mode, compare queries to the top X references [Default: 1]
rliterman@0 82 n_ref = 1
rliterman@0 83
rliterman@0 84 // If the assembly file contains the string <trim_name>, remove it from the sample name (e.g. '_contigs_skesa')
rliterman@0 85 trim_name = '""'
rliterman@0 86
rliterman@0 87 // If running SNP pipeline, set the maximum percent of isolates with missing data allowed in the final alignment/distances [Default: 50]
rliterman@0 88 max_missing = 50
rliterman@0 89
rliterman@0 90 // Alternate directory for pybedtools tmp files [Default: "" (system default)]
rliterman@0 91 tmp_dir = ""
rliterman@0 92
rliterman@0 93 // Set IDs for isolates to exclude from analysis (Comma-separated list)
rliterman@0 94 exclude = ""
rliterman@0 95
rliterman@0 96 // By default, do not perform edge-filtered SNP rescuing
rliterman@0 97 rescue = "norescue"
rliterman@0 98
rliterman@0 99 // Help function
rliterman@0 100 help = "nohelp"
rliterman@0 101 h = "nohelp"
rliterman@0 102 }