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comparison nextflow.tmpl @ 0:8e7a84e62b43 draft

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planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd
author galaxytrakr
date Fri, 13 Mar 2026 21:22:16 +0000
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-1:000000000000 0:8e7a84e62b43
1 /*
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 CSP2 Nextflow config file (for Dev25)
4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5 */
6
7 profiles {
8 standard {
9 process.executor = 'local'
10 params.cores = @CORES@
11 params.python_module = ""
12 params.mummer_module = ""
13 params.skesa_module = ""
14 params.bedtools_module= ""
15 params.mash_module = ""
16 params.bbtools_module = ""
17 }
18 }
19
20 process {
21 cpus = @CORES@
22
23 withLabel: 'mummerMem' {
24 label = 'mummerMem'
25 cpus = 1
26 memory = '4 GB'
27 }
28 withLabel: 'skesaMem' {
29 label = 'skesaMem'
30 memory = '12 GB'
31 }
32 }
33
34
35 // Global default params
36 params {
37
38 // Setting output directory
39
40 // Set name for output folder/file prefixes
41 out = "CSP2_${new java.util.Date().getTime()}"
42
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]
44 outroot = ""
45
46 // CSP2 can run in the following run-modes:
47
48 // assemble: Assemble read data (--reads/--ref_reads) into FASTA via SKESA (ignores --fasta/--ref_fasta/--snpdiffs)
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)
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
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
52
53 runmode = ""
54
55 // Location for isolate sequence data
56 reads = ""
57 fasta = ""
58
59 // Location for reference sequence data
60 ref_reads = ""
61 ref_fasta = ""
62
63 // IDs for reference sequences (Comma-separated list)
64 ref_id = ""
65
66 // Location for snpdiffs files
67 snpdiffs = ""
68
69 // Read read_info
70 readext = "fastq.gz"
71 forward = "_1.fastq.gz"
72 reverse = "_2.fastq.gz"
73
74 ref_readext = "fastq.gz"
75 ref_forward = "_1.fastq.gz"
76 ref_reverse = "_2.fastq.gz"
77
78 // Analytical variables
79
80 // Only consider queries if the reference genome is covered by at least <min_cov>% [Default: 85]
81 min_cov = 85
82
83 // Only consider SNPs from contig alignments longer than <min_len> bp [Default: 500]
84 min_len = 500
85
86 // Only consider SNPs from contig alignments with <min_iden>% identity [Default: 99]
87 min_iden = 99
88
89 // Remove SNPs that occur within <ref_edge>bp from the end of the reference contig [Default: 150]
90 ref_edge = 150
91
92 // Remove SNPs that occur within <query_edge>bp from the end of the query contig [Default: 150]
93 query_edge = 150
94
95 // SNP density filters: Given density windows provided by dwin, purge windows where more than the allowable window SNPs (wsnps) are found
96 // Default: 3 max per 1000bp, 2 max per 125bp, 1 max per 15bp, filtered from biggest window to smallest
97 // Set --dwin 0 to disable density filtering
98 dwin = "1000,125,15"
99 wsnps = "3,2,1"
100
101 // If running refchooser in snp mode, compare queries to the top X references [Default: 1]
102 n_ref = 1
103
104 // If the assembly file contains the string <trim_name>, remove it from the sample name (e.g. '_contigs_skesa')
105 trim_name = '""'
106
107 // If running SNP pipeline, set the maximum percent of isolates with missing data allowed in the final alignment/distances [Default: 50]
108 max_missing = 50
109
110 // Alternate directory for pybedtools tmp files [Default: "" (system default)]
111 tmp_dir = ""
112
113 // Set IDs for isolates to exclude from analysis (Comma-separated list)
114 exclude = ""
115
116 // By default, do not perform edge-filtered SNP rescuing
117 rescue = "norescue"
118
119 // Help function
120 help = "nohelp"
121 h = "nohelp"
122
123 // Bootstrap settings for iqTree
124 notree = "none" // Dummy setting to skip tree-building
125 b = 0 // Nonparametric bootstrap replicates
126 bb = 1000 // Ultrafast bootstrap replicates
127 model = "MFP+MERGE+ASC" // iqTree model
128 }