# Common parameters
THREADS: 16

# FASTQ inputs
CONTIG_FASTQ_1:
  class: File
  location: ../Data/SRR27548858_1.fastq.gz

CONTIG_FASTQ_2:
  class: File
  location: ../Data/SRR27548858_2.fastq.gz

MAP_FASTQ_1:
  class: File
  location: ../Data/SRR27548858_1.fastq.gz

MAP_FASTQ_2:
  class: File
  location: ../Data/SRR27548858_2.fastq.gz

# trimming parameters
TRIM_QUALITY: 20
TRIM_TAIL: 1

# MEGAHIT outputs
MEGAHIT_OUTPUT_DIR: contigSRR20140048

# annotation settings
EVALUE: 0.1

BLASTN_rRNA_FASTA_FILE1:
  class: File
  location: ../Data/SILVA_138.1_LSUParc_tax_silva.fasta.gz

BLASTN_rRNA_FASTA_FILE2:
  class: File
  location: ../Data/SILVA_138.1_SSUParc_tax_silva.fasta.gz

DIAMOND_FASTA_FILE:
  class: File
  location: ../Data/uniprot_sprot.fasta.gz

GTF_FILE_NAME: contigSRR20140048_annotation.gtf
