Troubleshooting

General troubleshooting guide for the EpiDiverse analysis pipelines

Singularity issues

Sometimes Singularity runs into problems when pulling multiple images at the same time for a pipeline run. In these instances it is sometimes better to pull the images manually into the directory that the pipeline will be run from, using for instance the following code:

singularity pull --name epidiverse-[PIPELINE]-[VERSION].simg \
docker://epidiverse/[PIPELINE]:[VERSION]

Check the Nextflow Documentation for more information about configuring Singularity

Extra resources and getting help

If you still have an issue with running the pipeline then feel free to contact us at [e-mail] or by opening an issue in the respective pipeline repository on GitHub asking for help.

If you have problems that are directly related to Nextflow and not our pipelines then check out the Nextflow gitter channel or the google group.