fastqrepair

nf-core/fastqrepair is a specialized bioinformatics pipeline designed to handle and repair corrupted or non-compliant FASTQ/FASTQ.gz files, which are commonly used in genomic sequencing data analysis. The pipeline addresses several critical data quality issues: it recovers reads from corrupted gzipped FASTQ files, ensures recovered reads are well-formed, re-pairs reads that have become disordered, and removes unpaired reads. The workflow integrates several established tools: `gzrt` for recovering data from corrupted gzip files, `wipertools` (from fastqwiper) for making reads well-formed, `bbmap/repair.sh` for re-pairing reads, `FastQC` for quality control checks, and `MultiQC` for aggregating and reporting QC results. This combination allows users to transform messy sequencing data into clean, analysis-ready FASTQ files accompanied by comprehensive quality control reports. To use the pipeline, users prepare a samplesheet CSV file specifying sample names and corresponding FASTQ file paths (supporting both single-end and paired-end data). The pipeline is executed via Nextflow, supporting various profiles for different computing environments (local, Docker, Singularity, Conda, etc.). It produces clean FASTQ files and detailed textual reports of the cleaning actions performed. The project is part of the nf-core community-curated pipeline framework, ensuring standardized, reproducible, and well-documented bioinformatics workflows.