nf-core-koreaworkshop
AWS nextflow workshop for the 19th Korean Genome Organization (KOGO) Winter Symposium (Jan 31. - Feb 1.)
Science Score: 31.0%
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
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○.zenodo.json file
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✓DOI references
Found 7 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 (9.2%) to scientific vocabulary
Repository
AWS nextflow workshop for the 19th Korean Genome Organization (KOGO) Winter Symposium (Jan 31. - Feb 1.)
Basic Info
- Host: GitHub
- Owner: yuukiiwa
- License: mit
- Language: Nextflow
- Default Branch: master
- Size: 2.22 MB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Introduction
nf-core/koreaworkshop is a hands-on exercise for the nextflow training at the Korean Genome Organization (KOGO) Winter Symposium. This pipeline will contain the following functionalities:
- Alignment with minimap2
- Read statistics with samtools
Prior to the workshop (Feb 1.) please install the following software
Java v11+
Check whether it is installed with the following:
java -version
nextflow
``` wget https://github.com/nextflow-io/nextflow/releases/download/v23.10.0/nextflow chmod +x nextflow ./nextflow
mv nextflow ~/bin/ # move nextflow to your user path or you can also execute nextflow by typing the path to nextflow
```
nf-core tools
pip install nf-core
docker
Please follow the instruction on https://docs.docker.com/engine/install/ to install docker.
Check whether it is installed with the following:
docker info
repository clone
git clone https://github.com/yuukiiwa/nf-core-koreaworkshop.git
if you encounter any problem with the installation, please look for Yuk Kei (likely in a red hoodie and a yellow backpack) after the talks on Jan 31. between 17:20-18:00. We will set up a table at KOGO for potential troubleshooting.
Running the pipeline
We will use the following samplesheet.csv for the pipeline:
wget https://raw.githubusercontent.com/yuukiiwa/nf-core-koreaworkshop/master/samplesheet.csv
We will use the following samples for the pipeline:
wget https://github.com/nf-core/test-datasets/blob/nanoseq/reference/GRCh38_EDIL3.fa
You can run the pipeline with the following command:
./nextflow nf-core-koreaworkshop/main.nf --input nf-core-koreaworkshop/samplesheet.csv --outdir output --fasta GRCh38_EDIL3.fa -profile docker
When the pipeline is done running, it should look like the following:
Support
If you missed the workshop or were not able to be in KOGO or need more clarification after the KOGO workshop, the nf-core outreach team will organize 90-min, small-group zoom training sessions on nextflow. Please stay tuned for the dates we will be holding the zoom training sessions.
Credits
nf-core/koreaworkshop was originally written by Yuk Kei Wan.
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: Yuk Kei Wan
- Login: yuukiiwa
- Kind: user
- Website: https://yuukiiwa.github.io/
- Repositories: 4
- Profile: https://github.com/yuukiiwa
:octocat: gave me a :panda_face: profile pic. I like trains a lot especially those in very intricate networks.
Citation (CITATIONS.md)
# nf-core/koreaworkshop: 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.
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