A lightweight and flexible Nextflow pipeline for trimming single-end and paired-end FASTQ files using Fastp, with automatic MultiQC report generation and metadata handling via a sample sheet.
- 🧬 Accepts both SE and PE reads
- 🚀 Runs with Singularity on SLURM HPC
- 📊 MultiQC summary report
- 📝 Output summary CSV for downstream use
git clone https://github.com/your-username/nf-fastp.git
Create a CSV file named samplesheet.csv in the root directory of the repository. The sample sheet should contain the following columns:
sample_id,species,fastq_1,fastq_2
S1,human,/absolute/path/S1_R1.fastq.gz,/absolute/path/S1_R2.fastq.gz
S2,mouse,/absolute/path/S2_R1.fastq.gz,nextflow run nf-fastp/ \
--samplesheet ./samplesheet.csv \
--outdir ./results \
-profile slurm \
-resumeA MultiQC report is generated for the fastp runs. Inspect the multiqc_report.html file for fastp stats. This file is located in ./results/multiqc/
Summary files in csv format are generated for each sample and a single all_samples_summary.csv is also created. These files contain sample_id and total_reads columns.