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params.yml
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params.yml
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# ============================= Input =======================================
reads_type: "raw" # "raw" or "clean"
input_contigs: false # false or path to contigs file
# ============================= Output ======================================
outdir: "output"
# ============================= Optional steps switch =======================================
use_abricate: false
use_decontam: false
use_dram: false
use_eggnog: false
use_iphop: false
use_kraken2: false
use_phamb: false
# ============================= Optional steps parameters =======================================
# kraken2 + bracken
kraken2_db: "viral"
kraken2_clean: true
save_output_fastqs : false
save_reads_assignment : false
# Decontamination
decontam_min_similarity: 0.95
contamref_idx: "/project/genomics/jru/data2/db/viroprofiler/contamination_refs/hg19/ref"
# ============================= Contig library ==============================
assembler: "spades"
assemblies: "scaffolds" # [contigs, scaffolds]
contig_minlen: 5000
contig_cluster_min_similarity: 95 # 0-100
contig_cluster_min_coverage: 85 # 0-100
# ============================= Gene library ==============================
prot_cluster_min_similarity: 0.7 # Minimum similarity of protein AA seqs in the same cluster
prot_cluster_min_coverage: 0.9 # Minimum similarity of protein AA seqs in the same cluster
gene_cluster_min_similarity: 0.9 # Minimum similarity of gene DNA seqs in the same cluster
gene_cluster_min_coverage: 0.9 # Minimum similarity of gene DNA seqs in the same cluster
# ============================= Binning =====================================
binning: false # "phamb", "vrhyme" or false
binning_minlen_contig: 5000
binning_minlen_bin: 5000
dvf_qvalue: 0.1
# ============================= Viral detection =============================
# virsorter2_groups: "dsDNAphage,NCLDV,RNA,ssDNA,lavidaviridae"
virsorter2_groups: "dsDNAphage"
# ============================= Taxonomy ====================================
contig_minlen_vcontact2: 10000
pc_inflation: 1.5
vc_inflation: 1.5
taxa_db_source: "NCBI"
# ============================= Replication cycle ===========================
replicyc: "bacphlip" # "replidec" or "bacphlip"