Pitagora Workflows in CWL

This repository is to share the Common Workflow Language definition files of tools and workflows, maintained by Pitagora Network, as known as Galaxy Community Japan.

Tools

• Get Data
  • download-sra
  • fastq-dump
  • pfastq-dump
• Data Formatting
  • samtools
• Read Alignment
  • bwa
  • bowtie
  • bowtie2
  • last
  • star
  • HISAT2
• Variant Analysis
  • gatk
  • annovar
  • picard
• Transcriptome Analysis
  • splice junction mapper
    • tophat2
  • transcript assemble / quantification
    • cufflinks
    • stringtie
    • eXpress
    • rsem
    • rsubread
    • kallisto
    • sailfish
    • salmon
  • de novo transcriptome assemble
    • trinity

Workflows

• RNA-Seq
  • TopHat2-*
    • tophat2-cufflinks
  • HISAT2-*
    • hisat2-cufflinks
    • hisat2-stringtie
  • STAR-*
    • star-cufflinks
    • star-stringtie
    • star-rsem
  • kallisto
  • sailfish
  • salmon