Hello All, when trying to run the initial test run of viralrecon using nextflow run nf-core/viralrecon -r 2.6.0 -profile test,singularity --outdir test on a new HPC cluster I am getting an error with singularity pulling samtools. It suggests increasing the pull timeout but this is occurring in a couple seconds and the current pull timeout is 20 minutes. I don’t know if this matters but the only difference between this working on another cluster with nextflow and singularity preinstalled and modules and this new cluster is I used conda to install singularity. conda install bioconda::nextflow conda install conda-forge::singularity

can you run the singularity pull command manually?

if i run singularity pull --name depot.galaxyproject.org-singularity-samtools-1.16.1--h6899075_1.img.pulling.1760709096397 https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1 > /dev/null I get ERROR: pull is only supported for shub URIs

from what I see is the singularity version via conda outdated. any chance your admins could install apptainer instead?