TronFlow alignment pipeline

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RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Workflow for Spliced RNAseq data Steps:

• workflow_quality.cwl:
• FastQC (Read Quality Control)
• fastp (Read Trimming)
• STAR (Read mapping)
• featurecounts (transcript read counts)
• kallisto (transcript [pseudo]counts)