This repository contains the Common Workflow Language (CWL) definitions of the workflows introduced in the book #NGS_DAT 2nd edition (A tutorial book in Japanese, 次世代シークエンサー DRY 解析教本 改訂第 2 版).
This repository provides workflows of the Level 2 section of the NGS_DAT 2nd edition.
- disease-genome
- 疾患ゲノム解析 (p.64)
- by @tom-tan
- no test
- rna-seq
- 発現解析 (p.86)
- by @ykohki
- epigenome-chip-seq
- エピゲノム解析 (ChIP-seq) (p.114)
- by @suecharo
- epigenome-bs-seq
- エピゲノム解析 (BS-seq) (p.164)
- by @manabuishii
- meta16s-seq
- メタゲノム解析 (p.203)
- by @inutano
- no test
- bacteria-genome
- バクテリアゲノム解析 (p.246)
- by @suecharo
- animal-genome-assembly
- 動物ゲノムアセンブリ (p.274)
- by @inutano
- transcriptome-assembly
- トランスクリプトームアセンブル解析 (p.309)
- by @yyoshiaki
For more detailed documentation on testing, see test/README.md.
There are many online documents to learn about CWL out there:
- The official website
- Getting started
- Getting started in Japanese
- The workflow meetup Tokyo/Osaka
- Slack workspace and invitation code is on the website
- Pitagora Network
- a monthly meetup in Tokyo for bioinformatics workflow users and developers
p.333 に記載のある URL https://tinyurl.com/dat2_cwl_example がアクセス不能となっています。すみません。
こちらで指定すべきコマンドと URL はこちらです。(コピペする場合は $ は除いてください)
$ cwltool https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/workflow/meta16s-seq/meta16s-seq.demo.cwl
Please create an issue on github issue if you have any trouble with the workflows. For questions to Common Workflow Language, please go to discourse group of CWL - the experts will help you.
Copyright (c) 2020 Contributors. See LICENSE for further details.