TronFlow

TronFlow is an open source collection of computational workflows originally conceived for tumor-normal somatic variant calling over whole exome data and the manipulation of BAM and VCF files with the aim of having comparable and analysis-ready data. Over time, we have extended it to germline variant calling, copy numbers and other related technologies and analyses.

Its modular architecture covers different analytical and methodological use cases that allow analysing FASTQ files into analysis-ready and comparable results. They can be used independently or in combination. The workflows are implemented in the Nextflow framework (Di Tommaso, 2017) and inspired by the community effort in NF-core (Ewels, 2020). They use conda environments which enable a seamless installation, easy integration with cluster queue managers and ensure the reproducibility of results. Using tabular files as an interface to each module facilitate batch processing. The normalisation of variants and homogeneous technical annotations enable the comparison of variant calls from different pipelines.

TronFlow workflows are publicly available on GitHub and open-sourced under the MIT license. We actively seek feedback from the community to make the workflow robust to different use cases and datasets.

https://tronflow-docs.readthedocs.io/en/latest/