Worked on the nf-core/methylseq repository to address a critical issue affecting pipeline robustness during alignment and deduplication when bwameth was enabled without a provided FASTA index. Focused on improving error handling by updating the pipeline’s logic in Groovy and Nextflow, ensuring that missing FASTA index scenarios no longer caused markduplicate failures or unclear error messages. Enhanced the documentation using Markdown to clarify expected behavior and guide users in diagnosing and resolving related issues. This targeted bug fix improved the reliability of the bioinformatics pipeline and provided clearer guidance for users working with bwameth in methylation sequencing workflows.