https://github.com/inutano/pitagora-cwl
Common Workflow Language tools and workflows by Pitagora-Network
Science Score: 10.0%
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Low similarity (3.5%) to scientific vocabulary
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Common Workflow Language tools and workflows by Pitagora-Network
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Fork of pitagora-network/pitagora-cwl
Created about 7 years ago
· Last pushed almost 7 years ago
https://github.com/inutano/pitagora-cwl/blob/master/
# Pitagora Workflows in CWL
[](https://zenodo.org/badge/latestdoi/172622089)
This repository is to share the [Common Workflow Language](https://www.commonwl.org) definition files of tools and workflows, maintained by Pitagora Network, as known as Galaxy Community Japan.
## Tools
- Get Data
- [download-sra](tools/download-sra)
- [fastq-dump](tools/fastq-dump)
- [pfastq-dump](tools/pfastq-dump)
- Data Formatting
- [samtools](tools/samtools)
- Read Alignment
- [bwa](tools/bwa)
- [bowtie](tools/bowtie)
- [bowtie2](tools/bowtie2)
- [last](tools/last)
- [star](tools/star)
- [HISAT2](tools/hisat2)
- Variant Analysis
- [gatk](tools/gatk)
- [annovar](tools/annovar)
- [picard](tools/picard)
- Transcriptome Analysis
- splice junction mapper
- [tophat2](tools/tophat2)
- transcript assemble / quantification
- [cufflinks](tools/cufflinks)
- [stringtie](tools/stringtie)
- [eXpress](tools/eXpress)
- [rsem](tools/rsem)
- [rsubread](tools/rsubread)
- [kallisto](tools/kallisto)
- [sailfish](tools/sailfish)
- [salmon](tools/salmon)
- de novo transcriptome assemble
- [trinity](tools/trinity)
## Workflows
See documentation in each workflow directory for the instruction.
- RNA-Seq
- TopHat2-*
- [tophat2-cufflinks](workflows/tophat2-cufflinks)
- HISAT2-*
- [hisat2-cufflinks](workflows/hisat2-cufflinks)
- [hisat2-stringtie](workflows/hisat2-stringtie)
- STAR-*
- [star-cufflinks](workflows/star-cufflinks)
- [star-stringtie](workflows/star-stringtie)
- [star-rsem](workflows/star-rsem)
- [kallisto](workflows/kallisto)
- [sailfish](workflows/sailfish)
- [salmon](workflows/salmon)
Owner
- Name: Tazro Inutano Ohta
- Login: inutano
- Kind: user
- Location: Tokyo
- Company: @DBCLS
- Website: https://orcid.org/0000-0003-3777-5945
- Twitter: inutano
- Repositories: 58
- Profile: https://github.com/inutano
#WeAreHackersWeDance