A Nextflow pipeline for de novo eukaryotic transcriptome assembly.

This pipeline processes paired-end RNA-seq data through multiple steps to generate a high-quality transcriptome assembly:

1. Trimming: Removes adapters and low-quality sequences using fastp
2. Quality Control: Ensures proper read pairing and quality using seqkit
3. Merging: Combines reads from multiple samples into a single dataset
4. Normalization: Reduces redundancy via digital normalization with BBNorm
5. Assembly: Assembles transcripts using either rnaSPAdes or Trinity
6. Quality Assessment: Evaluates completeness using BUSCO

• Nextflow (21.10.0+)
• Conda or Mamba for dependency management
• Input file listing samples in tab-separated format

No installation required other than Nextflow and Conda. The pipeline will automatically create the necessary environment with all dependencies.

# If you don't have mamba installed (recommended for faster conda installations)
conda install -c conda-forge mamba

# Clone the repository
git clone https://github.com/jakeelamb/nf-denovo-transcriptome.git
cd nf-denovo-transcriptome

# Run with rnaSPAdes
nextflow run main.nf -profile slurm --assembler rnaspades

# Run with Trinity
nextflow run main.nf -profile slurm --assembler trinity

# With custom parameters
nextflow run main.nf --input my_samples.txt --outdir /path/to/results --kmer_size 27

Create a tab-separated file (default: samples.txt) with columns:

sample_id    /path/to/R1.fastq.gz    /path/to/R2.fastq.gz