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Debugging develop mode with Nextflow

Tips for debugging develop mode.

Input files are not found


This is common for nf-core pipelines that use a sample sheets, like nf-core/rnaseq.

If the pipeline you are running uses input files that aren't passed through a Nextflow input channel, they need to be in the shared file system and referenced using an absolute path.

For example, "/Volumes/flowdeploy-shared/file.txt" on your Mac needs to be "/Volumes/flowdeploy-shared/file.txt" in the sample sheet.

Nextflow freezes

Always run nextflow run outside of the shared file system. Nextflow can hit a deadlock when run from within the shared file system, causing the pipeline to freeze.

Nextflow work directories can have broken symlinks if the mount point differs between machines. Ensure consistent mount points to avoid this limitation; we enforce a consistent mount point name to autocorrect most potential failures.

No Docker Container

Processes within FlowDeploy require a Docker container. The provided configuration includes a global default if a process does not specify a Docker container.