nextflow.config

conda.enabled = true
conda.createTimeout = '2 h'

profiles {
 ramdisk {
   def username = System.getProperty("user.name")
   conda.cacheDir = "/dev/shm/${username}/nf-conda-cacheDir/"
   singularity.cacheDir = "/dev/shm/${username}/nf-singularity-cacheDir/"
 }
}

includeConfig './modules/dna_features_viewer/nextflow.config'
//includeConfig './conf/apptainer.nf.config' // This enables Apptainer (academic fork of Singularity), and sets some bespoke paths for my own HPC node
includeConfig './conf/singularity.nf.config' // This enables Singularity (company fork of Singularity), and sets some bespoke paths for my own HPC node

params.renaming = "$projectDir/dataset/renaming.tsv" //I think, this sets a default. Can be overwrote with CLI. See here for details: https://www.nextflow.io/docs/latest/sharing.html#:~:text=projectDir%20implicit%20variable

manifest {
 mainScript = 'interproscan_parallel.nf'
 defaultBranch = 'main'
 description = 'A wrapper pipeline that runs, simplifies, and plots an interproscan analysis of a polypetide fasta'
 version = '1.0.0'
}

dag.file = "results/${manifest.mainScript}__dag.html"
dag {
    enabled = true
    overwrite = true
}

trace.file = "results/${manifest.mainScript}__trace.txt"
trace {
    enabled = true
    overwrite = true
}

report.file = "results/${manifest.mainScript}__report.html"
report {
    enabled = true
    overwrite = true
}

executor {
  queueSize = 20
}

process {
    // This container is used to get around this error
    // bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
    // Per ldd --version, the host GLIBC version is 2.17 
    // Within the container, the GLIBC version is 2.31
    // BUT, the current version of interproscan is interproscan-5.64-96.0 (just released today...), the docker container hasn't been updated yet. 
    // See: https://hub.docker.com/r/interpro/interproscan/tags
    interpro_scan_container = 'docker://interpro/interproscan:5.73-104.0'
    withName:interproscan_run {
        container = interpro_scan_container
    }
    withName:download_interproscan_docker_data {
        container = interpro_scan_container
    }
}

//singularity or apptainer.runOptions need to be set to nothing for the download_data subworkflow to work
//*.runOptions is currently being overridden by download.config