sunbeam_config.yml

# 
# Sunbeam configuration file, customized for NEON soil shotgun metagenomics dataset
#
# Defining samples:
#   Run 'sunbeam list_samples <data_dir>' to create a list of samples and
#   associated fastq.gz files. Samples must be in gzipped fastq format.
#
# Paths:
#   Paths are resolved through the following rules:
#     1. If the path is absolute, the path is parsed as-is
#     2. If the path is not absolute, the path at 'root' is appended to it
#     3. If the path is not 'output_fp', the path is checked to ensure it exists
#
# Suffixes:
#   Each subsection contains a 'suffix' key that defines the folder under
#   'output_fp' where the results of that section are put.
# General options
all:
  root: /projectnb2/talbot-lab-data/zrwerbin/metagenomes_raw/manuscript_test/metagenome_analysis/
  output_fp: sunbeam_output
  samplelist_fp: samples.csv
  paired_end: true
  download_reads: false
  version: 2.1.1+dev81.gd0e29cd

# Quality control
qc:
  suffix: qc
  # Sample intake
  seq_id_ending: ''
  # Trimmomatic
  threads: 4
  java_heapsize: 512M
  leading: 3
  trailing: 3
  slidingwindow: [4, 15]
  minlen: 36
  adapter_template: $CONDA_PREFIX/share/trimmomatic/adapters/NexteraPE-PE.fa
  # Cutadapt
  fwd_adapters: [CTGAAGCT, TAATGCGC, GTTTCCCAGTCACGATC]
  rev_adapters: [ACGTCCTG, GTCAGTAC, GTTTCCCAGTCACGATC]
  # Komplexity
  kz_threshold: 0.55
  # Decontam.py
  pct_id: 0.5
  frac: 0.6
  host_fp: 'PhiX'


# Taxonomic classifications
classify:
  suffix: classify
  threads: 4
  #kraken_db_fp: 'kraken_pluspf'
  kraken_db_fp: '/projectnb2/microbiome/kraken2_db/kraken_pluspf'

# Contig assembly
assembly:
  suffix: assembly
  min_length: 1000
  threads: 14

# Contig annotation
annotation:
  suffix: annotation
  min_contig_len: 1000
  circular_kmin: 10
  circular_kmax: 1000
  circular_min_len: 3500

blast:
  threads: 14

blastdbs:
  root_fp: ''  
  protein:
    ncyc: 'db/NCyc/NCyc_unique.fasta'
    card: 'db/card/protein_fasta_protein_homolog_model.fasta'    

mapping:
  suffix: mapping
  genomes_fp: ''
  samtools_opts: ''
  threads: 14

download:
  suffix: download
  threads: 4

sbx_metaquast:
  threads: 4

sbx_binning:
  threads: 28
  min_contig_length: 1500
 
maxbin: 
  markerset: 107