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1 | 1 | { |
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3 | | - "https://w3id.org/ro/crate/1.1/context", |
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22 | 22 | "@id": "./", |
23 | 23 | "@type": "Dataset", |
24 | 24 | "creativeWorkStatus": "Stable", |
25 | | - "datePublished": "2026-05-27T11:44:13+00:00", |
| 25 | + "datePublished": "2026-07-23T15:20:45+00:00", |
26 | 26 | "description": "#  \n\n[](https://github.com/codespaces/new/nf-cmgg/sampletracking)\n[](https://github.com/nf-cmgg/sampletracking/actions/workflows/nf-test.yml)\n[](https://github.com/nf-cmgg/sampletracking/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.4.1)\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-cmgg/sampletracking)\n\n## Introduction\n\n**nf-cmgg/sampletracking** is a bioinformatics pipeline that performs sampletracking on sequencing samples. The pipeline does this by crosschecking SNP fingerprints and by checking if the expected sex matches the real sex of the sample.\n\n\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,pool,sex,sample_bam,sample_bam_index,snp_bam,snp_bam_index\nSAMPLE1,POOL1,F,SAMPLE1.bam,SAMPLE1.bam.bai,SAMPLE1_snp.cram,SAMPLE2_snp.cram.crai\n```\n\nEach row represents a sample annotated with the pool it was sequenced in and the expected sex of this sample. It also needs a BAM/CRAM file with the sample data and (optionally) a FASTQ/BAM/CRAM file with SNP tracking data for the sample. Crosschecking fingerprints will be skipped when no SNP tracking data is provided.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-cmgg/sampletracking \\\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\n## Credits\n\nnf-cmgg/sampletracking was originally written by [@matthdsm](https://github.com/matthdsm).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@nvnieuwk](https://github.com/nvnieuwk)\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## Development environment\n\nA [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:\n\n```\npixi install\n```\n\nThen run `pixi shell` to enter the environment and start developing.\n\n## Citations\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 uses 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).\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", |
27 | 27 | "hasPart": [ |
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105 | 105 | "name": "nf-cmgg/sampletracking" |
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134 | 134 | "dateCreated": "", |
135 | | - "dateModified": "2026-05-27T13:44:13Z", |
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