A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks.

This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O.

By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.

Based on a pipeline by Sydney Informatics Hub:

...

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)

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control.

Alignment, assembly and annotation of generated transcripts from RNASEQ reads.

Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.

Alignment, assembly RNASEQ reads and annotation of generated transcripts.

Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).