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Running a workflow

In order to run a nextflow workflow, you will need three to four things:

  • the workflow (usually a .nf file)
  • a config file for talking to the cluster
  • a file with parameters
  • (optional) other parameters supplied directly to the nextflow command

In principle, when using the workflows in this repository, you will not have to worry about the workflow file or the run.config files. Those files specify the order of processes and how to talk to a slurm cluster and generally do not change across different projects.

Setup

The most important file for you to edit is the params.yml file that contains all the information that you need to adjust to your specific system. See the Setup documentation for guidance on how to edit this file.

Execution

Once you have your input data and params.yml file ready, you can then run the workflow like this:

module load java/18.0.2.1
module load nextflow/22.10.5

nextflow run </path/to/this/repo>/workflows/preprocessing.nf \
	-c </path/to/this/repo>/config/run.config \
	-params-file ./params.yml \
	-with-trace -with-report

Second project

If you want to run the same preprocessing then for a different project, simply duplicate the params.yml file and adjust the output and samples parameter and you can just run the same workflow on your new data like this:

module load java/18.0.2.1
module load nextflow/22.10.5

nextflow run </path/to/this/repo>/workflows/preprocessing.nf \
	-c </path/to/this/repo>/config/run.config \
	-params-file ./params_new_project.yml \
	-with-trace -with-report

Please note that you can run only a single nextflow workflow at the same time from the same directory. Nextflow will lock the current working directory ( from which you called nextflow run and no other workflow can be started while the other one is still running).

Troubleshooting

It might happen that you run into an unforeseen problem and one of the processes that nextflow is managing for you errors out. If so, nextflow will tell you which process ran into an error and where you can find the corresponding logs. Each process gets assigned a working directory with a unique hash in the work folder. For example, the output of nextflow might look like this:

executor >  slurm (79)
[54/a2ce3b] process > binning_prep (BINNING_PREP ... [100%] 12 of 12 ✔
[f3/33b63b] process > metabat (METABAT on D04_T2)    [100%] 12 of 12 ✔
[46/dbf5b9] process > maxbin (MAXBIN on D04_T2)      [100%] 12 of 12 ✔
[95/193f4e] process > concoct (CONCOCT on D04_T1)    [ 91%] 11 of 12
[e3/9f45b7] process > dastool (DASTool on D04_T1)    [ 91%] 11 of 12, failed:...
[e1/f745aa] process > checkm (CheckM on D02_T2)      [100%] 10 of 10
[b9/09b2d2] process > gtdbtk (GTDB-tk on D02_T2)     [100%] 10 of 10
[e3/9f45b7] NOTE: Process `dastool (DASTool on D04_T1)` terminated with an error exit status (1) -- Execution is retried (1)

It makes sense to check out the log files in this folder to figure out what is going on:

cd ./work/e3/9f45b7<tab>
ls -l

Please note that the actual folder name is much longer, but you can just use autocomplete to find the correct folder for the process that errored out.