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nf_mini

development stage. Mini modules from things I feel its a pain to find again all the time

Guidelines:

IMPORTANT !:

  • Only use containers - so can be reused on cluster (no other than containers)
  • Configuration labels per module : standardized with håkons labels !
  • standardization all format as Håkons for reusability
  • all DSL2 !!

Workflows

with detailed submodules

Usage

testing usage

On SAGA

To use solely an image: use apptainer

  • local images on saga: /cluster/projects/nn9305k]$ cd nextflow/singularity_img/
  • containers that can be used: see 
IMG=<image_path/name.sif> 
apptainer shell $IMAGE 
# then you can use the commands

# To bind directories
# apptainer shell --bind <your_dir>,<another_your_dir>:<path_in_container> my_container.sif
apptainer shell --bind /opt,/data:/mnt my_container.sif

See here if you need more to bind paths to the container (so you can see the files you are working with) https://apptainer.org/docs/user/latest/bind_paths_and_mounts.html