[BUG] Offline running on computecanada generally does not work

[AntoineTheb]

Description of the bug

I've had several issues trying to run sf-tractomics on computecanada's clusters.

1: The documentation has a few errors:
https://scilus.github.io/sf-tractomics/guides/nointernet/

The command to download the images (nf-core download ...) gives an error. I had to see alliancecan's wiki to actually set up the nf-core environment (https://docs.alliancecan.ca/wiki/Nextflow) and download the images.

2: Actually forcing nextflow to be offline did not work using several tricks. Simply pointing to the pulled pipeline did not work and nextflow still tried to pull things off the internet, and timeout after a very long time. Setting the flag "-offline" after "nextflow run" did not work. Eventually, I found out that I had to set the environment flag NXF_OFFLINE='true' to prevent nextflow from trying to access internet.

3: The filename of the cached images is wrong:

Notice how the offline pipeline tries to pull images even though their are downloaded and in the right folder because the filename is wrong (extraneous/missing docker-io prefix)

4: Trying to use the 'slurm' profile, nextflow can't find which RAC account to use

5: Without the slurm profile, nextflow can't make use of the node's resources ? See my script below, I get

Command used and terminal output

#!/bin/bash
#SBATCH --time=3:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24 
#SBATCH --cpus-per-task=8
#SBATCH --mem=0
#SBATCH --account=def-descotea

set -x 

cd $SCRATCH

module load python/3.11
source nf-core-env/bin/activate
module load apptainer
module load nextflow

export NXF_OFFLINE='true'
export NXF_SINGULARITY_CACHEDIR=$SCRATCH/NXF_SINGULARITY_CACHEDIR
export NXF_APPTAINER_CACHEDIR=$SCRATCH/NXF_APPTAINER_CACHEDIR
export SINGULARITY_CACHEDIR=$SCRATCH/SINGULARITY_CACHEDIR
export APPTAINER_CACHEDIR=$SCRATCH/APPTAINER_CACHEDIR
export SLURM_ACCOUNT=def-descotea

nextflow run $SCRATCH/scilus-sf-tractomics_dev/dev -resume -offline -profile singularity,slurm \
  --input /home/thea1603/projects/rrg-descotea/processing/bundleparc/hcp105/derivatives/sf-tractomics/input/samplesheet.csv --outdir $SCRATCH/sf-tractomics_hcp105 --run_topup false --run_pft_tracking false --run_local_tracking false --account def-descotea

Relevant files

No response

System information

Trying to run stuff on rorqual