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BU-ISCIII / buisciii-tools

set of helper tools for bu-isciii management of its core services portfolio.
GNU General Public License v3.0
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Check path where nexflow downloads the needed singularity images #269

Closed jaimeozaez closed 1 month ago

jaimeozaez commented 1 month ago

We expect every nf-core pipeline to use the necessary singularity-images from /data/bi/pipelines/singularity-images/, and this is the path where the news singularity-images should be downloaded. We have this path configured (or we will have it un a near future) in our ~/.bashrc file, but this path can be "overwritten" by some nextflow config files.

Example case: For viralrecon, we have the following lines added at the /data/bi/pipelines/nf-core-viralrecon-2.6.0/workflow/nextflow.config file:

// Added by `nf-core download` v2.3.dev0 //
singularity.cacheDir = "${projectDir}/../singularity-images/"
///////////////////////////////////////%

This triggers the pipeline to use the images from /data/bi/pipelines/nf-core-viralrecon-2.6.0/workflow/../singularity-images/ and downloading the missing ones inside this path, instead of doing it in the correct path.

This lines must be removed from all the config files (in all nf-core pipelines).

saramonzon commented 1 month ago

changed in pipelines_new this should be fixed once pipelines_new becames the new pipelines