DAT2-CWL

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).

Workflows

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.

Learn how to run CWL

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

Erratum

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

Troubleshooting

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

Copyright (c) 2020 Contributors. See LICENSE for further details.

Release

• 1.1.0
  • at Mar 28, 2022
• 1.0.1
  • at Nov 24, 2021
• 1.0.0
  • at Dec 4, 2019