forked from qbic-pipelines/rnadeseq
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow_schema.json
238 lines (238 loc) · 10.8 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
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/master/nextflow_schema.json",
"title": "qbic-pipelines/rnadeseq pipeline parameters",
"description": "Differential gene expression analysis and pathway analysis of RNAseq data",
"type": "object",
"definitions": {
"mandatory_arguments": {
"title": "Mandatory arguments",
"type": "object",
"fa_icon": "fas fa-terminal",
"properties": {
"gene_counts": {
"type": "string",
"description": "If input_type = featurecounts: Raw count table (TSV). Columns are samples and rows are genes. 1st column Ensembl_ID, 2nd column gene_name. If input_type = rsem or input_type = salmon: Path to rsem/salmon output folder."
},
"metadata": {
"type": "string",
"description": "Metadata table (TSV). Rows are samples and columns contain sample grouping."
},
"model": {
"type": "string",
"description": "Linear model function to calculate the contrasts (TXT). Variable names should be columns in metadata file."
},
"project_summary": {
"type": "string",
"description": "Project summary file downloaded from the qPortal."
},
"multiqc": {
"type": "string",
"description": "multiqc.zip folder containing the multiQC plots and report."
}
},
"required": ["metadata", "model", "project_summary", "multiqc", "gene_counts"]
},
"options": {
"title": "Options",
"type": "object",
"description": "",
"default": "",
"properties": {
"contrast_matrix": {
"type": "string",
"default": "DEFAULT",
"description": "Tsv indicating which contrasts to consider, one contrast per column. 1 or 0 for every coefficient of the linear model. Check contrasts docs."
},
"contrast_list": {
"type": "string",
"default": "DEFAULT1",
"description": "Tsv indicating list of the contrasts to calculate. 3 columns: factor name, contrast numerator and denominator. Check contrasts docs."
},
"contrast_pairs": {
"type": "string",
"default": "DEFAULT2",
"description": "Tsv indicating list of contrast pairs to calculate. 3 columns: contrast name, numerator and denominator. Check contrasts docs."
},
"relevel": {
"type": "string",
"default": "NO_FILE2",
"description": "Tsv indicating list of factors (conditions in the metadata table) and the new level on which to relevel the factor. Check contrasts docs."
},
"logFCthreshold": {
"type": "integer",
"default": 0,
"description": "Threshold (int) to apply to Log 2 Fold Change to consider a gene as differentially expressed."
},
"genelist": {
"type": "string",
"default": "NO_FILE",
"description": "Txt file with list of genes (one per line) of which to plot heatmaps for normalized counts across all samples."
},
"batch_effect": {
"type": "string",
"default": "false",
"description": "Turn on this flag if you wish to consider batch effects. You need to add the batch effect to the linear model too!"
},
"quote": {
"type": "string",
"default": "NO_FILE4",
"description": "Signed copy of the offer."
},
"min_DEG_pathway": {
"type": "integer",
"default": 1,
"description": "Integer indicating how many genes in a pathway must be differentially expressed to be considered as enriched, and report these pathways in tables and the final report. The default value is 1."
},
"vst_genes_number": {
"type": "integer",
"default": 1000,
"description": "Integer indicating how many genes to subset to during vst transformation (when using rlog, will ignore this number). Default: 1000."
},
"skip_pathway_analysis": {
"type": "boolean",
"default": false,
"description": "Turn on this flag if you wish to skip pathway analysis."
},
"use_vst": {
"type": "boolean",
"default": false,
"description": "Set this flag to true to use vst transformation (recommended when >50 samples; if false, will use rlog)"
}
}
},
"other_options": {
"title": "Other options",
"type": "object",
"description": "",
"default": "",
"properties": {
"outdir": {
"type": "string",
"description": "The output directory where the results will be saved",
"default": "./results",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits",
"default": "false"
},
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle"
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"hidden": true
},
"tracedir": {
"type": "string",
"default": "./results/pipeline_info",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"custom_config_version": {
"type": "string",
"default": "master",
"description": "Git commit id for Institutional configs.",
"hidden": true
},
"custom_config_base": {
"type": "string",
"default": "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}",
"description": "Base directory for Institutional configs.",
"hidden": true
},
"config_profile_description": {
"type": "string",
"default": "false",
"description": "Institutional config description.",
"hidden": true
},
"config_profile_contact": {
"type": "string",
"default": "false",
"description": "Institutional config contact information.",
"hidden": true
},
"config_profile_url": {
"type": "string",
"default": "false",
"description": "Institutional config URL link.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/mandatory_arguments"
},
{
"$ref": "#/definitions/options"
},
{
"$ref": "#/definitions/other_options"
}
],
"properties": {
"show_hidden_params": {
"type": "boolean"
},
"input_type": {
"type": "string",
"default": "featurecounts",
"description": "Which type of input is provided, one of featurecounts, rsem, salmon"
},
"genome": {
"type": "string",
"default": null,
"description": "Which genome to use for analysis, e.g. GRCh37; see /conf/igenomes.config for which genomes are available."
},
"gtf": {
"type": "string",
"default": null,
"description": "Not necessary if genome is set. GTF file to be used for DESeq if input is rsem or salmon, not necessary for featurecounts."
},
"organism": {
"type": "string",
"default": null,
"description": "Not necessary if genome is set. Which organism name to use for pathway analysis, e.g. `hsapiens`, not necessary if `--skip_pathway_analysis = true`."
},
"library": {
"type": "string",
"default": null,
"description": "Not necessary if genome is set. Which bioconductor library to use for pathway analysis, e.g. org.Hs.eg.db, not necessary if --skip_pathway_analysis = true."
},
"keytype": {
"type": "string",
"default": null,
"description": "Not necessary if genome is set. Which keytype to use for pathway analysis, e.g. ENSEMBL, not necessary if --skip_pathway_analysis = true."
},
"igenomes_base": {
"type": "string",
"default": "s3://ngi-igenomes/igenomes"
},
"igenomes_ignore": {
"type": "boolean",
"default": false
}
}
}