Tidying up after Nextflow

You will have noticed that along with the results directory, viralrecon and all nf-core pipelines produce a work directory. This directory contains the results from each job run as part of the pipeline and is what Nextflow uses to resume a pipeline if something goes wrong and the pipeline doesn’t complete successfully . Once the pipeline has run successfully, then we no longer need the work directory so we can delete it, especially as it can take up a lot of space. We can check how much space the work directory is using with the du command:

du -sh work

You’ll see that, even for just five samples, the pipeline created over 4Gb of data! You can remove the directory with the rm command:

rm -rf work