Translating Galaxy to Nextflow

Galaxy to Nextflow

• Tool - Samtools Flagstat
  • Sections
  • Introduction
  • Running Janis Translate
  • Manual Adjustments
  • Running Samtools Flagstat as a Workflow
  • Conclusion
• Workflow - RNAseq Reads to Counts
  • Sections
  • Introduction
  • Running Janis Translate
  • Task 1: Swapping Containers
  • Task 2: Removing COLLECTION_COLUMN_JOIN process
  • Task 3: Setting up Inputs
  • Task 4: Fixing RSEQC Input
  • Task 5: FASTQC outdir
  • Task 6: CUTADAPT output collection
  • Task 7: HISAT2 index
  • Task 8: FEATURECOUNTS command
  • Task 9: PICARD_MARK_DUPLICATES command
  • Task 10: MULTIQC input filename collision
  • Task 11: MULTIQC script (final task)
  • Completed Workflow
  • Conclusion