params {
  config_profile_name = 'Cell-free DNA test'
  max_cpus = 20
  max_memory = 30.GB
  max_time = 5.h

  // Input data
  single_end = false
  input_paths = [
['Lib1', ['/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/1_L001-ds.3f368de895fc4b06b9556e9188628a0f/1_S1_L001_R1_001.fastq.gz', '/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/1_L001-ds.3f368de895fc4b06b9556e9188628a0f/1_S1_L001_R2_001.fastq.gz']],
['Lib2', ['/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/2_L001-ds.a161ac826e794a74bcdd9ae84011ddb5/2_S2_L001_R1_001.fastq.gz', '/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/2_L001-ds.a161ac826e794a74bcdd9ae84011ddb5/2_S2_L001_R2_001.fastq.gz']],
['Lib3', ['/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/3_L001-ds.2986ba7469ad444e9de867c55240b9ba/3_S3_L001_R1_001.fastq.gz', '/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/3_L001-ds.2986ba7469ad444e9de867c55240b9ba/3_S3_L001_R2_001.fastq.gz']],
['Lib4', ['/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/4_L001-ds.150388f12ed643679e76ff0d61eb7242/4_S4_L001_R1_001.fastq.gz', '/home/agalicina/tmp/DimaTO/cfdna-235942708/FASTQ_Generation_2021-08-27_22_52_17Z-453924997/4_L001-ds.150388f12ed643679e76ff0d61eb7242/4_S4_L001_R2_001.fastq.gz']]
]

  // Genome references
  fasta = '/home/agalicina/GENOMES/HG38_FASTA/hg38.fa'
  fasta_index = '/home/agalicina/GENOMES/HG38_FASTA/hg38.fa.fai'
	bismark_index = 'results/reference_genome/BismarkIndex/' 
  // Ignore `--input` as otherwise the parameter validation will throw an error
  schema_ignore_params = 'genomes,input_paths,input'

  cytosine_report = true
  save_reference = true
  comprehensive = true
	skip_deduplication = true
}