-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathro-crate-metadata.json
295 lines (295 loc) · 15.9 KB
/
ro-crate-metadata.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
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
{
"@context": [
"https://w3id.org/ro/crate/1.1/context",
{
"GithubService": "https://w3id.org/ro/terms/test#GithubService",
"JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
"PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
"TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
"TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
"TestService": "https://w3id.org/ro/terms/test#TestService",
"TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
"TravisService": "https://w3id.org/ro/terms/test#TravisService",
"definition": "https://w3id.org/ro/terms/test#definition",
"engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
"instance": "https://w3id.org/ro/terms/test#instance",
"resource": "https://w3id.org/ro/terms/test#resource",
"runsOn": "https://w3id.org/ro/terms/test#runsOn"
}
],
"@graph": [
{
"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
"datePublished": "2024-12-16T07:20:17+00:00",
"description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinfamilies_logo_dark.png\">\n <img alt=\"nf-core/proteinfamilies\" src=\"docs/images/nf-core-proteinfamilies_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/proteinfamilies/actions/workflows/ci.yml)\n[](https://github.com/nf-core/proteinfamilies/actions/workflows/linting.yml)[](https://nf-co.re/proteinfamilies/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinfamilies)\n\n[](https://nfcore.slack.com/channels/proteinfamilies)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinfamilies** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/proteinfamilies \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinfamilies/usage) and the [parameter documentation](https://nf-co.re/proteinfamilies/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinfamilies/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinfamilies/output).\n\n## Credits\n\nnf-core/proteinfamilies was originally written by Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinfamilies` channel](https://nfcore.slack.com/channels/proteinfamilies) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/proteinfamilies for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
"hasPart": [
{
"@id": "main.nf"
},
{
"@id": "assets/"
},
{
"@id": "conf/"
},
{
"@id": "docs/"
},
{
"@id": "docs/images/"
},
{
"@id": "modules/"
},
{
"@id": "modules/nf-core/"
},
{
"@id": "workflows/"
},
{
"@id": "subworkflows/"
},
{
"@id": "nextflow.config"
},
{
"@id": "README.md"
},
{
"@id": "nextflow_schema.json"
},
{
"@id": "CHANGELOG.md"
},
{
"@id": "LICENSE"
},
{
"@id": "CODE_OF_CONDUCT.md"
},
{
"@id": "CITATIONS.md"
},
{
"@id": "modules.json"
},
{
"@id": "docs/usage.md"
},
{
"@id": "docs/output.md"
},
{
"@id": ".nf-core.yml"
},
{
"@id": ".pre-commit-config.yaml"
},
{
"@id": ".prettierignore"
}
],
"isBasedOn": "https://github.com/nf-core/proteinfamilies",
"license": "MIT",
"mainEntity": {
"@id": "main.nf"
},
"mentions": [
{
"@id": "#b4774fae-81ac-4414-83cb-ec9cf45b27da"
}
],
"name": "nf-core/proteinfamilies"
},
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
]
},
{
"@id": "main.nf",
"@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
"dateCreated": "",
"dateModified": "2024-12-16T07:20:17Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": ["nf-core", "nextflow"],
"license": ["MIT"],
"name": ["nf-core/proteinfamilies"],
"programmingLanguage": {
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
},
"sdPublisher": {
"@id": "https://nf-co.re/"
},
"url": ["https://github.com/nf-core/proteinfamilies", "https://nf-co.re/proteinfamilies/dev/"],
"version": ["1.0.0dev"]
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
"@type": "ComputerLanguage",
"identifier": {
"@id": "https://www.nextflow.io/"
},
"name": "Nextflow",
"url": {
"@id": "https://www.nextflow.io/"
},
"version": "!>=24.04.2"
},
{
"@id": "#b4774fae-81ac-4414-83cb-ec9cf45b27da",
"@type": "TestSuite",
"instance": [
{
"@id": "#a04b9235-f9ed-4286-ab1b-c5ab9f1fca7c"
}
],
"mainEntity": {
"@id": "main.nf"
},
"name": "Test suite for nf-core/proteinfamilies"
},
{
"@id": "#a04b9235-f9ed-4286-ab1b-c5ab9f1fca7c",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/proteinfamilies",
"resource": "repos/nf-core/proteinfamilies/actions/workflows/ci.yml",
"runsOn": {
"@id": "https://w3id.org/ro/terms/test#GithubService"
},
"url": "https://api.github.com"
},
{
"@id": "https://w3id.org/ro/terms/test#GithubService",
"@type": "TestService",
"name": "Github Actions",
"url": {
"@id": "https://github.com"
}
},
{
"@id": "assets/",
"@type": "Dataset",
"description": "Additional files"
},
{
"@id": "conf/",
"@type": "Dataset",
"description": "Configuration files"
},
{
"@id": "docs/",
"@type": "Dataset",
"description": "Markdown files for documenting the pipeline"
},
{
"@id": "docs/images/",
"@type": "Dataset",
"description": "Images for the documentation files"
},
{
"@id": "modules/",
"@type": "Dataset",
"description": "Modules used by the pipeline"
},
{
"@id": "modules/nf-core/",
"@type": "Dataset",
"description": "nf-core modules"
},
{
"@id": "workflows/",
"@type": "Dataset",
"description": "Main pipeline workflows to be executed in main.nf"
},
{
"@id": "subworkflows/",
"@type": "Dataset",
"description": "Smaller subworkflows"
},
{
"@id": "nextflow.config",
"@type": "File",
"description": "Main Nextflow configuration file"
},
{
"@id": "README.md",
"@type": "File",
"description": "Basic pipeline usage information"
},
{
"@id": "nextflow_schema.json",
"@type": "File",
"description": "JSON schema for pipeline parameter specification"
},
{
"@id": "CHANGELOG.md",
"@type": "File",
"description": "Information on changes made to the pipeline"
},
{
"@id": "LICENSE",
"@type": "File",
"description": "The license - should be MIT"
},
{
"@id": "CODE_OF_CONDUCT.md",
"@type": "File",
"description": "The nf-core code of conduct"
},
{
"@id": "CITATIONS.md",
"@type": "File",
"description": "Citations needed when using the pipeline"
},
{
"@id": "modules.json",
"@type": "File",
"description": "Version information for modules from nf-core/modules"
},
{
"@id": "docs/usage.md",
"@type": "File",
"description": "Usage documentation"
},
{
"@id": "docs/output.md",
"@type": "File",
"description": "Output documentation"
},
{
"@id": ".nf-core.yml",
"@type": "File",
"description": "nf-core configuration file, configuring template features and linting rules"
},
{
"@id": ".pre-commit-config.yaml",
"@type": "File",
"description": "Configuration file for pre-commit hooks"
},
{
"@id": ".prettierignore",
"@type": "File",
"description": "Ignore file for prettier"
},
{
"@id": "https://nf-co.re/",
"@type": "Organization",
"name": "nf-core",
"url": "https://nf-co.re/"
}
]
}