Science Score: 57.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 10 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary
Repository
Nextflow implementation of scge workflow
Basic Info
- Host: GitHub
- Owner: dhslab
- License: mit
- Language: Nextflow
- Default Branch: dev
- Size: 328 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
Introduction
nf-core/scge is a bioinformatics pipeline that ...
- Runs tumor normal dragen
- Get Indels
- Get Transgene Junctions
- Annotate Transgene Variants
- Annotate sv, cnv, hard-filtered vcf
- Makes vep to tsv file
- Makes scge report
Usage
To run at dragen step, prepare a samplesheet with the following columns:
dragen_samplesheet.csv:
csv
id,uid,sample_type,fastq_list,hotspot_file
tumor_sample_1,tumor_sample_1,tumor,/path/to/fastqlist,/path/to/hotspot_1
normal_sample,tumor_sample_1,normal,/path/to/fastqlist,/path/to/hotspot_1
tumor_sample_2,tumor_sample_2,tumor,/path/to/fastqlist,/path/to/hotspot_2
normal_sample,tumor_sample_2,normal,/path/to/fastqlist,/path/to/hotspot_2
The hotspot file is optional.
To run the pipeline from the analysis step: prepare a samplesheet with the following columns:
analysis_samplesheet.csv:
csv
id,dragen_path,hotspot_file
sample1,/path/to/dragen_output/sample1,/path/to/hotspot_1
sample2,/path/to/dragen_output/sample2,/path/to/hotspot_2
Now, you can run the pipeline using:
bash
nextflow run dhslab/nf-core-scge \
-profile ris,<dragen2/dragen4/dragenaws> \
--input /path/to/samplesheet \
--outdir <OUTDIR>
Additional arguments:
--hotspot_bed - /path/to/hotspot.bed
[!WARNING] Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow option can be used to provide any configuration except for parameters; see docs.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
Pipeline output
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
Credits
nf-core/scge was originally written by Nidhi.
We thank the following people for their extensive assistance in the development of this pipeline:
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on the Slack #scge channel (you can join with this invite).
Citations
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
You can cite the nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Owner
- Name: Code and Software from David Spencer's lab
- Login: dhslab
- Kind: organization
- Email: dspencerlab@gmail.com
- Location: United States of America
- Website: davidspencerlab.org
- Twitter: dspencerlab
- Repositories: 6
- Profile: https://github.com/dhslab
Citation (CITATIONS.md)
# nf-core/scge: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. ## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. ## Pipeline tools - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
GitHub Events
Total
- Issues event: 2
- Push event: 22
- Pull request event: 1
- Create event: 2
Last Year
- Issues event: 2
- Push event: 22
- Pull request event: 1
- Create event: 2
Dependencies
- actions/upload-artifact v4 composite
- seqeralabs/action-tower-launch v2 composite
- actions/upload-artifact v4 composite
- seqeralabs/action-tower-launch v2 composite
- mshick/add-pr-comment v2 composite
- actions/checkout v4 composite
- nf-core/setup-nextflow v1 composite
- actions/stale v9 composite
- actions/setup-python v5 composite
- eWaterCycle/setup-singularity v7 composite
- nf-core/setup-nextflow v1 composite
- actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
- actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
- peter-evans/create-or-update-comment 71345be0265236311c031f5c7866368bd1eff043 composite
- actions/checkout v4 composite
- actions/setup-python v5 composite
- actions/upload-artifact v4 composite
- nf-core/setup-nextflow v1 composite
- dawidd6/action-download-artifact v3 composite
- marocchino/sticky-pull-request-comment v2 composite
- actions/setup-python v5 composite
- rzr/fediverse-action master composite
- zentered/bluesky-post-action v0.1.0 composite
- multiqc 1.19.*
- fastqc 0.12.1.*
- multiqc 1.19.*