Specific Questions

[thomasmanke]

Nextflow basics

• output
• label processes --> resource allocation
• run own workflows from github - multiple per repo?
• overwrite ~HOME/.nextflow
• modularization

Epi2Me

• where are the containers
• how to add new process to existing pipeline (e.g samtools flagstat)

nf-core

• use profile
• use (institutional) configs -> how to set cluster config
• use parameter-file (configure with nf-core launch)
• manage genomes (using iGenomes)

[adRn-s]

profiles {
    
    deep22 {
       
        cleanup = true
    
        process {
            executor = 'slurm'
            queue = 'test'
        }
       
        executor {
            queueSize = 8
            pollInterval = '1 min'
            queueStatInterval = '5 min'
        }
        
        // $NXF_SINGULARITY_CACHEDIR should be set in either ~/.bash{rc,_profile}
        // to stop downloading the same image for every run.
        // For example, we have: /localenv/pipegrp/nxf/apptainer
        // together  with: ln -s /localenv/pipegrp/nxf/home ~/.nextflow
        singularity {
            enabled = true
            autoMounts = true
        }
       
        params {
            config_profile_description = 'Config profile tu run Apptainer at MPI-IE Freiburg.'
            max_memory = 50.GB
            max_cpus = 20
            max_time = 24.h
            // https://github.com/bioinfo-pf-curie/geniac-template/blob/master/conf/test.config
        }
    }
      
    debug {
        cleanup = false
    }
}

I had this nextflow.cfg from a previous effort, it might be useful... Good luck!