# For single-run assemblies, uncomment the following block
# Use reads1 only for single-end and both reads1 and reads2 for paired-end 
'''
reads1:
  class: File
  format: http://edamontology.org/format_1930
  path: /path/to/reads1

reads2: # OPTIONAL
  class: File
  format: http://edamontology.org/format_1930
  path: /path/to/reads2
'''

# For co-assemblies, uncomment the following block
# Use multiple_reads_1 for multiple single-end samples, 
# jointly with multiple_reads_2 for multiple paired-end combinations
'''
multiple_reads_1:
  - class: File
    format: http://edamontology.org/format_1930
    path: /path/to/fastq_1.gz
  - class: File
    format: http://edamontology.org/format_1930
    path: /path/to/fastq_2.gz

multiple_reads_2: # OPTIONAL
  - class: File
    format: http://edamontology.org/format_1930
    path: /path/to/fastq_1.gz
  - class: File
    format: http://edamontology.org/format_1930
    path: /path/to/fastq_2.gz
'''

assembler: 'megahit' # OR 'metaspades'

prefix: # ASSEMBLY PREFIX e.g. 'SRR6257420'

min_contig_length: 500

host_genome:
  class: File
  format: http://edamontology.org/format_1929
  path: /path/to/host_genome

# Genome for host decontamination. Name must match the bwa index name
database_flag: 
  - #STRING e.g. 'phiX'

coassembly: 'no' # OR 'yes'

blastdb_dir:
  class: Directory
  path: /path/to/blast_databases

assembly_version: # STRING FOR ASSEMBLY NAME / VERSION e.g. '001'

raw_dir_name: # STRING FOR RAW FILES OUTPUT DIRECTORY e.g. 'raw'