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Common Nextflow errors

Common Nextflow errors

Owned by Marie-Emilie Gauthier
Last updated: Jun 28, 2024
1 min read

1. Nextflow pipeline stickied on revision

If a new pipeline version was released you might get the following error:

Project `eresearchqut/ontvisc` is currently stickied on revision: dev -- you need to explicitly specify a revision with the option `-r` in order to use it

You have 2 options:

  • If you want to keep a copy of the old version that works in your assets then just add the -r parameter and specify the version you would like to run in your nextflow command

nextflow run eresearchqut/ontvisc -r dev

  • The other option is to delete the old version from your nextflow cache located under ~/.nextflow/assets.

rm -rf ~/.nextflow/assets/eresearchqut/ontvisc

2. Compilation error

ERROR ~ Script compilation error - file : /home/gauthiem/code/github/troubleshooting/dev/ontvisc/main.nf - cause: Unexpected input: '{' @ line 382, column 29. process MAPPING_BACK_TO_REF { ^ 1 error -- Check '.nextflow.log' file for details

This generally means there is a bug in the code included between the brackets for this process and it is unable to compile.

Check your code carefully for any typos.

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