To aid reproducibility, I have incorporated conda environments into each process in the nextflow script. It does make it run slightly slower as the relevant software needs to be installed but it ensure all runs use the same version of each software. However, I cannot get multiqc to install via bioconda on the server so I have left this out of the conda environment ( I thought it doesn't really matter which version you us anyway as it displays summary results rather than changing data).
To aid reproducibility, I have incorporated conda environments into each process in the nextflow script. It does make it run slightly slower as the relevant software needs to be installed but it ensure all runs use the same version of each software. However, I cannot get multiqc to install via bioconda on the server so I have left this out of the conda environment ( I thought it doesn't really matter which version you us anyway as it displays summary results rather than changing data).