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planemo upload commit 2a16aa1a872336561378f55b9b3ecd74dcfcfcbc
author galaxytrakr
date Thu, 19 Mar 2026 15:32:21 +0000
parents 8e7a84e62b43
children
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1 /*
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2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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3 CSP2 Nextflow config file (for Dev25)
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4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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5 */
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6
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7 profiles {
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8 standard {
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9 process.executor = 'local'
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10 params.cores = @CORES@
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11 params.python_module = ""
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12 params.mummer_module = ""
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13 params.skesa_module = ""
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14 params.bedtools_module= ""
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15 params.mash_module = ""
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16 params.bbtools_module = ""
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17 }
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18 }
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19
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20 process {
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21 cpus = @CORES@
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22
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23 withLabel: 'mummerMem' {
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24 label = 'mummerMem'
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25 cpus = 1
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26 memory = '4 GB'
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27 }
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28 withLabel: 'skesaMem' {
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29 label = 'skesaMem'
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30 memory = '12 GB'
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31 }
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32 }
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33
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34
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35 // Global default params
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36 params {
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37
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38 // Setting output directory
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39
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40 // Set name for output folder/file prefixes
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41 out = "CSP2_${new java.util.Date().getTime()}"
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42
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43 // Set output parent directory [Default: CWD; Set this to have all output go to the same parent folder, with unique IDs set by --out]
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44 outroot = ""
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45
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46 // CSP2 can run in the following run-modes:
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47
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48 // assemble: Assemble read data (--reads/--ref_reads) into FASTA via SKESA (ignores --fasta/--ref_fasta/--snpdiffs)
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49 // align: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta), run MUMmer alignment analysis for each query/ref combination (ignores --snpdiffs)
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50 // 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
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51 // 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
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52
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53 runmode = ""
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54
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55 // Location for isolate sequence data
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56 reads = ""
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57 fasta = ""
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58
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59 // Location for reference sequence data
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60 ref_reads = ""
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61 ref_fasta = ""
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62
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63 // IDs for reference sequences (Comma-separated list)
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64 ref_id = ""
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65
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66 // Location for snpdiffs files
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67 snpdiffs = ""
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68
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69 // Read read_info
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70 readext = "fastq.gz"
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71 forward = "_1.fastq.gz"
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72 reverse = "_2.fastq.gz"
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73
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74 ref_readext = "fastq.gz"
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75 ref_forward = "_1.fastq.gz"
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76 ref_reverse = "_2.fastq.gz"
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77
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78 // Analytical variables
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79
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80 // Only consider queries if the reference genome is covered by at least <min_cov>% [Default: 85]
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81 min_cov = 85
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82
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83 // Only consider SNPs from contig alignments longer than <min_len> bp [Default: 500]
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84 min_len = 500
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85
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86 // Only consider SNPs from contig alignments with <min_iden>% identity [Default: 99]
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87 min_iden = 99
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88
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89 // Remove SNPs that occur within <ref_edge>bp from the end of the reference contig [Default: 150]
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90 ref_edge = 150
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91
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92 // Remove SNPs that occur within <query_edge>bp from the end of the query contig [Default: 150]
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93 query_edge = 150
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94
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95 // SNP density filters: Given density windows provided by dwin, purge windows where more than the allowable window SNPs (wsnps) are found
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96 // Default: 3 max per 1000bp, 2 max per 125bp, 1 max per 15bp, filtered from biggest window to smallest
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97 // Set --dwin 0 to disable density filtering
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98 dwin = "1000,125,15"
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99 wsnps = "3,2,1"
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100
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101 // If running refchooser in snp mode, compare queries to the top X references [Default: 1]
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102 n_ref = 1
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103
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104 // If the assembly file contains the string <trim_name>, remove it from the sample name (e.g. '_contigs_skesa')
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105 trim_name = '""'
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106
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107 // If running SNP pipeline, set the maximum percent of isolates with missing data allowed in the final alignment/distances [Default: 50]
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108 max_missing = 50
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109
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110 // Alternate directory for pybedtools tmp files [Default: "" (system default)]
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111 tmp_dir = ""
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112
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113 // Set IDs for isolates to exclude from analysis (Comma-separated list)
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114 exclude = ""
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115
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116 // By default, do not perform edge-filtered SNP rescuing
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117 rescue = "norescue"
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118
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119 // Help function
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120 help = "nohelp"
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galaxytrakr
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121 h = "nohelp"
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galaxytrakr
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122
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123 // Bootstrap settings for iqTree
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124 notree = "none" // Dummy setting to skip tree-building
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125 b = 0 // Nonparametric bootstrap replicates
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126 bb = 1000 // Ultrafast bootstrap replicates
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127 model = "MFP+MERGE+ASC" // iqTree model
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128 }