config.yaml

run_name: PLATE_NAME
samplesheet: samplesheet.tsv
fastq_dir: "READS"

# Minimum gDNA read count to be passed to SPAdes
min_gDNA_read_count: 70000

# Minimum cDNA read count to be passed to Trinity
min_cDNA_read_count: 50000

# Minimum rRNA length to report in top blast hits vs pr2 DB
# This is the length of the blast alignment not the annotated gene
min_rRNA_blast_length: 500

# Interval to use for calculating random kmer uniquess (not currently reported in summary)
rku_gDNA_interval: 25000
rku_cDNA_interval: 25000

# Map gDNA reads against the corresponding genome assembly
map_gDNA: True

# Map cDNA reads against the corresponding genome assembly
map_cDNA: True

# Identity threshold for clustering transcriptome assembly
cdhit_identity_threshold: 0.98

# How many reads to classify using centrifuge [-u/--upto <int> stop after first <int> reads/pairs (no limit)]
centrifuge_upto: 1000000

# Paths to databases
bbduk_adapters: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/bbmap/resources/adapters.fa
pr2_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/pr2/5.0.0/pr2_version_5.0.0_SSU_taxo_long.fasta
diamond_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/diamond/reference_proteomes.dmnd
taxonomy_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/taxdump/fullnamelineage.dmp
kraken2_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/kraken2/
centrifuge_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/centrifuge/centrifugedb
centrifuge_NT_database: /ei/public/databases/centrifuge/ncbi/nt_20200707/nt