Cloud & HPC Genomics

// main.nf - DSL2 pipeline
nextflow.enable.dsl = 2

process BWA_MEM {
  tag "$meta.id"
  container "biocontainers/bwa-mem2:2.2.1"
  cpus 16
  memory "32 GB"

  input:
    tuple val(meta), path(reads)
    path reference

  output:
    tuple val(meta), path("*.bam")

  script:
  """
  bwa-mem2 mem -t ${task.cpus} ${reference} ${reads} \
    | samtools sort -@ 8 -o ${meta.id}.bam
  """
}

workflow {
  reads_ch = Channel.fromFilePairs(params.reads)
  ref_ch   = file(params.reference)
  BWA_MEM(reads_ch, ref_ch)
}

// Run: nextflow run main.nf --reads "data/*_{R1,R2}.fastq.gz" --reference hg38.fa -profile slurm