nextflow.config.bak

// settings to run diamond/blast
  params {
        tracedir = "pipeline_info"
        resdir = "nf-blast-results"
        query = ""
        db = "/project/aerc/ncbi/v5/nt"
        tax_db_dir = "/project/aerc/ncbi/v5"
        out = ""
        chunkSize = 250
        outfmtString = "6"
        evalue = "1e-10"
        targetSeqs = 50
        blastTask = 'blastn'
        blastOpts = ''
        diamondOpts = ''
      }

  manifest {
    name = 'blast-nf'
    author = 'Ido Bar'
    description = 'Homology search using BLAST or Diamond'
    mainScript = 'blast-nf.nf'
    nextflowVersion = '>=21.04.1'
    version = '0.1.0'
  }

  env {
        BLASTDB = "/project/aerc/ncbi/v5"
      }

  profiles {
        
    singularity {
        enabled = true
        autoMounts = true
        runOptions = '-B /project/aerc/ncbi/v5'
    }

    conda {
        process.conda = 'blast diamond'
    }
    blast_tax {
      params {
            query = ""
            db = "/project/aerc/ncbi/v5/nt"
            tax_db_dir = "/project/aerc/ncbi/v5"
            out = ""
            chunkSize = 250
            outfmtString = '6 std stitle staxids sscinames scomnames sskingdoms'
            evalue = "1e-10"
            targetSeqs = 50
            blastTask = 'blastn'
        }
    }
    diamond_tax {
      params {
            query = ""
            db = "/project/aerc/ncbi/v5/nr.dmnd"
            tax_db_dir = "/project/aerc/ncbi/v5"
            out = ""
            chunkSize = "250.KB"
            outfmtString = '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle staxids sscinames skingdoms sphylums'
            evalue = "1e-10"
            targetSeqs = 50
            blastTask = 'blastpD'
        }
    }
    test {
        params {
            query = "${launchDir}/test.fa"
            db = "/project/aerc/ncbi/v5/nt"
            tax_db_dir = "/project/aerc/ncbi/v5"
            out = "test.blastn.nt.outfmt6"
            chunkSize = 10
            outfmtString = "6"
            blastTask = 'blastn'
        }
    }
    test_tax {
        params {
            query = "${launchDir}/test.fa"
            db = "/project/aerc/ncbi/v5/nt"
            tax_db_dir = "/project/aerc/ncbi/v5"
            out = "test.blastn.nt.outfmt6"
            chunkSize = 10
            outfmtString = '6 std stitle staxids sscinames scomnames sskingdoms'
            blastTask = 'blastn'
        }
    }
    test_p {
        params {
            query = "test.faa"
            db = "/project/aerc/ncbi/v5/nr"
            tax_db_dir = "/project/aerc/ncbi/v5"
            out = "test.blastp.nr.outfmt6"
            chunkSize = 10
            blastTask = 'blastp'
        }
    }
    test_d {
        params {
            query = "test.faa"
            db = "/project/aerc/ncbi/v5/nr"
            tax_db_dir = "/project/aerc/ncbi/v5"
            outfmtString = '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle staxids sscinames skingdoms sphylums'
            out = "test.blastpD.nr.outfmt6"
            chunkSize = 20
            blastTask = 'blastpD'
            diamondOpts = '--fast'
        }
  }
}
  process {
        errorStrategy = { task.exitStatus in [143,137,104,134,139,271] ? 'retry' : 'finish' }
        maxRetries = 4

        withLabel: 'diamond' {
          cpus = { check_max( 4 + (2* task.attempt), 'cpus' ) }
          memory = { check_max( 14.GB + (2.GB * task.attempt), 'memory' ) }
          time = { check_max( 2.h + (2.h* task.attempt), 'time' ) }
          container = 'diamond_latest.sif'
        }
        withLabel: 'blast' {
          cpus = { check_max( 4 + (2 * task.attempt), 'cpus' ) }
          memory = { check_max( 6.GB + (2.GB * task.attempt), 'memory' ) }
          time = { check_max( 4.h + (2.h * task.attempt), 'time' ) }
          container = 'blast_latest.sif'
        }
        withName: 'diamond_prep_db' {
            time = { check_max( 7.h + (3.h * task.attempt), 'time' ) }
        }

    }


timeline {
  enabled = true
  file = "${params.resdir}/${params.tracedir}/${manifest.name}_${params.blastTask}_timeline.html"
}
report {
  enabled = true
  file = "${params.resdir}/${params.tracedir}/${manifest.name}_${params.blastTask}_report.html"
}
trace {
  enabled = true
  file = "${params.resdir}/${params.tracedir}/${manifest.name}_${params.blastTask}_trace.txt"
}
dag {
  enabled = true
  file = ( {nextflow.version.matches('22.04+')} ) ? "${params.resdir}/${params.tracedir}/${manifest.name}_${params.blastTask}_dag.mmd" : "${params.resdir}/${params.tracedir}/${manifest.name}_${params.blastTask}_dag.html"
  //file = "${params.resdir}/${params.tracedir}/${workflow.manifest.name}_${params.blastTask}_dag.html"
}


// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
  if (type == 'memory') {
    try {
      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
        return params.max_memory as nextflow.util.MemoryUnit
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
      return obj
    }
  } else if (type == 'time') {
    try {
      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
        return params.max_time as nextflow.util.Duration
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
      return obj
    }
  } else if (type == 'cpus') {
    try {
      return Math.min( obj, params.max_cpus as int )
    } catch (all) {
      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
      return obj
    }
  }
}