Translating Galaxy to NextflowΒΆ
- Tool - Samtools Flagstat
- 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