Chapter 9 Resuming the pipeline (Command line interface)

Nextflow provides a powerful command line interface for the execution pipelines.

As we have seen before a general way of running Nextflow looks like:

nextflow [options] COMMAND [arg...]

We often run the workflow using

nextflow main_19.nf --inputmzml "/crex/proj/uppmax2024-2-11/metabolomics/mzMLData/*.mzML" --qc 100

However, when Nextflow is run it will automatically use its powerful run command. So the above code can actually be run using:

nextflow run main_19.nf --inputmzml "/crex/proj/uppmax2024-2-11/metabolomics/mzMLData/*.mzML" --qc 100

The run command has several options that can be seen here

One the most important option is resume. This option executes the script using the cached results, useful to continue executions that was stopped by an error.

So if we imagine the above pipeline fails for example because of an error in one of the processes, after resolving the error, we can run the workflow using:

nextflow run main_19.nf -resume --inputmzml "/crex/proj/uppmax2024-2-11/metabolomics/mzMLData/*.mzML" --qc 100

Using this command, the already successfully executed processes will not be rerun. So the pipeline will continue from where it failed last time.

You can see the full description of Nextflow CLI here