-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathnextflow_schema.json
executable file
·111 lines (95 loc) · 4.36 KB
/
nextflow_schema.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/vonMeyennLab/nf_peakcalling/main/nextflow_schema.json",
"title": "Peak calling pipeline parameters",
"description": "Peak calling pipeline.",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"description": "Peak calling without control samples: List of input files in BAM/BED/BedGraph format or other format required by the peak caller, e.g. '*.bam' or '*.bedgraph'.\nPeak calling with control samples: A CSV file with the names of the treatment and control files in BAM/BED/BedGraph format or other format required by the peak caller, e.g. 'design.csv'.",
"help_text": "The CSV file should have the following format:\n\ntreatment,control\n/cluster/work/nme/data/josousa/project/SEQ01_H3K27me3_rep1.bam,/cluster/work/nme/data/josousa/project/SEQ01_input_rep1.bam\n/cluster/work/nme/data/josousa/project/SEQ01_H3K27me3_rep2.bam,/cluster/work/nme/data/josousa/project/SEQ01_input_rep2.bam\n/cluster/work/nme/data/josousa/project/SEQ01_H3K27me3_rep3.bam,/cluster/work/nme/data/josousa/project/SEQ01_input_rep3.bam",
"fa_icon": "fas fa-file-code"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use an absolute path.",
"fa_icon": "fas fa-folder-open"
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"required": ["genome"],
"description": "Reference genome used during alignment. This will provide MACS with the appropriate genome size.",
"properties": {
"genome": {
"type": "string",
"default": "Mus_musculus_GRCm39",
"description": "Name of the reference genome.",
"fa_icon": "fas fa-book",
"enum": ["Mus_musculus_GRCm39", "Mus_musculus_GRCm38_p6", "Homo_sapiens_GRCh38_p14", "Drosophila_melanogaster_BDGP6_46", "Caenorhabditis_elegans_WBcel235"]
}
}
},
"peak_caller_options": {
"title": "Peak caller options",
"type": "object",
"fa_icon": "fas fa-users-cog",
"description": "Choose the peak calling tool.",
"properties": {
"peak_caller": {
"type": "string",
"default": "macs",
"description": "Name of the peak calling tool.",
"fa_icon": "fas fa-book",
"enum": ["macs", "seacr"]
}
}
},
"module_arguments_options": {
"title": "Module arguments options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Add extra arguments to the workflow modules.",
"properties": {
"macs_callpeak_args": {
"type": "string",
"description": "MACS callpeak arguments.",
"fa_icon": "fas fa-file-code"
},
"seacr_args": {
"type": "string",
"description": "SEACR arguments.",
"fa_icon": "fas fa-file-code"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/peak_caller_options"
},
{
"$ref": "#/definitions/module_arguments_options"
}
]
}