regex101: nextflow

Regular Expression

process\s+(\w+|\"[^\"]+\"|'[^']+')\s*{((.|\n|\r)*)}

New

nextflow.enable.dsl=2

// params.module_dir = '.'
params.dbs_dir = '/mnt/OmicNAS/dd/alphafold/dbs'
params.max_template_date = '2020-05-14'
params.db_preset = 'reduced_dbs'
params.model_preset = 'monomer'
params.outdir = './'
params.cachedir = '/mnt/OmicNAS/cache/alphafold'

process ALPHAFOLD {
  conda "${moduleDir}/environment.yml"

  echo true

  maxForks 1

  stageInMode 'copy'

  storeDir "${params.cachedir}"

  publishDir "${params.outdir}", mode: 'copy'

  input:
    path fasta

  output:
    path "*", emit: outputs

  script:
    """
    python3 ${moduleDir}/docker/run_docker.py \
      --fasta_paths=${fasta} \
      --max_template_date=${params.max_template_date} \
      --model_preset=${params.model_preset} \
      --db_preset=${params.db_preset} \
      --data_dir=${params.dbs_dir} \
      --output_dir=\$PWD
    """
}

Substitution

nextflow.enable.dsl=2

// params.module_dir = '.'
params.dbs_dir = '/mnt/OmicNAS/dd/alphafold/dbs'
params.max_template_date = '2020-05-14'
params.db_preset = 'reduced_dbs'
params.model_preset = 'monomer'
params.outdir = './'
params.cachedir = '/mnt/OmicNAS/cache/alphafold'

process ALPHAFOLD {
  conda "${moduleDir}/environment.yml"

  echo true

  maxForks 1

  stageInMode 'copy'

  storeDir "${params.cachedir}"

  publishDir "${params.outdir}", mode: 'copy'

  input:
    path fasta

  output:
    path "*", emit: outputs

  script:
    """
    python3 ${moduleDir}/docker/run_docker.py \
      --fasta_paths=${fasta} \
      --max_template_date=${params.max_template_date} \
      --model_preset=${params.model_preset} \
      --db_preset=${params.db_preset} \
      --data_dir=${params.dbs_dir} \
      --output_dir=\$PWD
    """
}