-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy pathro-crate-metadata.json
323 lines (323 loc) · 16.1 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
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
{
"@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": "Stable",
"datePublished": "2025-01-15T09:03:36+00:00",
"description": "#  \n\n[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/ci.yml)\n[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.10812762)\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://tower.nf/launch?pipeline=https://github.com/qbic-pipelines/vcftomaf)\n\n## Introduction\n\n**qbic-pipelines/vcftomaf** is a bioinformatics pipeline that converts input Variant Call Format (vcf) files with one or two columns of (paired) samples to tabular Mutation Annotation Format (maf).\nThe resulting file(s) can be analyzed singly or as an entire cohort in R with [maftools](https://github.com/PoisonAlien/maftools).\n\n<p align=\"center\">\n <img title=\"Overview\" src=\"docs/images/metromap.png\" width=60%>\n</p>\n\n1. Optional Filtering of VCF files for PASS and / or with a target bed file ([`BCFtools`](https://github.com/samtools/bcftools))\n2. Optional liftover (needs a `chain` file, `--fasta` should refer to target genome version) ([`Picard LiftOverVCF`](https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard))\n3. Conversion from vcf to maf format([`vcf2maf`](https://github.com/mskcc/vcf2maf))\n4. Collect QC metrics and versions ([`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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,normal_id,vcf_normal_id,tumor_id,vcf_tumor_id,vcf,index\nmutect2_sample1,SAMPLE123,PATIENT1_SAMPLE123,SAMPLE456,PATIENT1_SAMPLE456,/path/to/vcf,/path/to/tbi\ntest2,control2,NORMAl,,,/path/to/vcf,/path/to/tbi\n```\n\nEach row represents a sample with one or two columns in the VCF file. The `normal_id` and `tumor_id` will be used for naming the columns in the MAF file. The `vcf_normal/tumor_id` refers to the sample name in the VCF file. This differs for each caller. For VCFs obtained from nf-core/sarek, the following is tested:\n\n| Caller | Normal ID | Tumor ID |\n| :------- | :---------------------- | :---------------------- |\n| Manta | NORMAL | TUMOR |\n| Mutect2 | {_patient_}_{\\_sample_} | {_patient_}_{\\_sample_} |\n| Strelka2 | NORMAL | TUMOR |\n\nThe values for _patient_ and _sample_ can be obtained from the nf-core/sarek samplesheet.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/vcftomaf \\\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**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](docs/usage.md) and the [parameter documentation](nextflow_schema.json).\n\nFor more details about the output files and reports, please refer to the\n[output documentation](docs/output.md).\n\n## Credits\n\nqbic-pipelines/vcftomaf was originally written by [SusiJo](https://github.com/SusiJo), [Friederike Hanssen](https://github.com/FriederikeHanssen) up to release 1.0.0. The pipeline was further developed by [Famke B\u00e4uerle](https://github.com/famosab) after release 1.0.0.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nIf you use qbic-pipelines/vcftomaf for your analysis, please cite it using the following doi: [10.5281/zenodo.10812762](https://zenodo.org/doi/10.5281/zenodo.10812762)\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\nThis pipeline is based on code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\nThe pipeline is currently maintained at QBiC and not an nf-core pipeline since it has not undergone nf-core community review.\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": "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/qbic-pipelines/vcftomaf",
"license": "MIT",
"mainEntity": {
"@id": "main.nf"
},
"mentions": [
{
"@id": "#3620cd02-07a3-4ffd-a6da-7423d4ac295c"
}
],
"name": "qbic-pipelines/vcftomaf"
},
{
"@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"
],
"creator": [
{
"@id": "https://orcid.org/0000-0003-1387-0251"
},
{
"@id": "#[email protected]"
}
],
"dateCreated": "",
"dateModified": "2025-01-15T10:03:36Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": [
"nf-core",
"nextflow"
],
"license": [
"MIT"
],
"name": [
"qbic-pipelines/vcftomaf"
],
"programmingLanguage": {
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
},
"sdPublisher": {
"@id": "https://nf-co.re/"
},
"url": [
"https://github.com/qbic-pipelines/vcftomaf",
"https://nf-co.re/qbic-pipelines/vcftomaf/1.2.0/"
],
"version": [
"1.2.0"
]
},
{
"@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": "#3620cd02-07a3-4ffd-a6da-7423d4ac295c",
"@type": "TestSuite",
"instance": [
{
"@id": "#29a20590-1b60-4510-8668-5dd0633a2175"
}
],
"mainEntity": {
"@id": "main.nf"
},
"name": "Test suite for qbic-pipelines/vcftomaf"
},
{
"@id": "#29a20590-1b60-4510-8668-5dd0633a2175",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing qbic-pipelines/vcftomaf",
"resource": "repos/qbic-pipelines/vcftomaf/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": "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/"
},
{
"@id": "https://orcid.org/0000-0003-1387-0251",
"@type": "Person",
"email": "[email protected]",
"name": "Famke B\u00e4uerle"
},
{
"@id": "#[email protected]",
"@type": "Person",
"email": "[email protected]",
"name": "Famke Ba\u0308uerle"
}
]
}