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config_template.yml
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config_template.yml
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#
# Sunbeam configuration file
#
# 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: "/home/zhaoc1/path/to/your/project/dir"
data_fp: "barcodes.txt"
output_fp: "sunbeam_output"
filename_fmt: "{sample}_{rp}.fastq"
subcores: 4
exclude: []
# Quality control
qc:
suffix: qc
# Trimmomatic
threads: 8
java_heapsize: 512M
leading: 3
trailing: 3
slidingwindow: [4,15]
minlen: 36
adapter_fp: "/home/zhaoc1/miniconda3/envs/sunbeam/share/trimmomatic/adapters/NexteraPE-PE.fa"
# Cutadapt
fwd_adapters: []
rev_adapters: []
# Decontam.py
pct_id: 0.5
frac: 0.6
keep_sam: False
method: bwa
human_genome_fp: "/mnt/isilon/microbiome/analysis/biodata/human_GRch38.fasta"
phix_genome_fp: "/mnt/isilon/microbiome/analysis/biodata/phix174.fasta"
# Taxonomic classifications
classify:
suffix: classify
threads: 8
kraken_db_fp: "/mnt/isilon/microbiome/analysis/biodata/krakendb/standard" # standard_erik
taxa_db_fp: ""
# Metaphlan2
metaphlan_fp: "/home/zhaoc1/sunbeam_neutrino/local/biobakery-metaphlan2-40d1bf693089"
mpa_pkl_fp: "/home/zhaoc1/sunbeam_neutrino/local/biobakery-metaphlan2-40d1bf693089/db_v20/mpa_v20_m200.pkl"
bt2_db_fp: "/home/zhaoc1/sunbeam_neutrino/local/biobakery-metaphlan2-40d1bf693089/db_v20/mpa_v20_m200"
# Contig assembly
assembly:
suffix: assembly
min_length: 300
threads: 8
cap3_fp: "/home/zhaoc1/sunbeam/local/CAP3"
# Contig annotation
annotation:
suffix: annotation
min_contig_len: 500
circular_kmin: 10
circular_kmax: 1000
circular_min_len: 3500
# Blast databases
blast:
threads: 8
blastdbs:
root_fp: "/mnt/isilon/microbiome/analysis/biodata/blast"
nucleotide:
# bacteria:
# bacteriaGenomes/ncbi_bacteria_20170330.fasta
# fungi:
# fungiGenomes/ncbi_fungi_20170330.fasta
# viral:
# viralGenomes/ncbi_nucl_viral_20170505.fasta
card:
card/nucleotide_fasta_protein_homolog_model.fasta
protein:
# integrase:
# UniprotPhageIntegrase.fasta
# aclame:
# ACLAME/aclame_proteins_viruses_prophages_0.4.fasta
# vfdb:
# VFDB/VFs.faa
viral:
add the refseq protein databases...
card:
card/protein_fasta_protein_homolog_model.fasta
mapping:
suffix: mapping
threads: 8
genomes_fp: "/mnt/isilon/microbiome/analysis/biodata/indexes"
Rscript_fp: "/home/zhaoc1/sunbeam_neutrino/local/bin"
# Pathfinder.py
rapsearch_fp: "/home/zhaoc1/sunbeam_neutrino/local/RAPSearch2/bin"
kegg_fp: "/mnt/isilon/microbiome/analysis/biodata/kegg"
kegg_idx_fp: "/mnt/isilon/microbiome/analysis/biodata/keggRAP"
kegg_to_ko_fp: "/mnt/isilon/microbiome/analysis/biodata/kegg2ko"
genomes_fp: "/mnt/isilon/microbiome/analysis/biodata/bowtie2/fungalIndexes"
bileacid_fp: "/mnt/isilon/microbiome/analysis/biodata/bileacidsIndexes"
glyco_fp: "/mnt/isilon/microbiome/analysis/biodata/diamondIndexes"
diamond_fp: "/home/zhaoc1/sunbeam_neutrino/local/diamond"
# contigs.rules
igv_fp: "/home/zhaoc1/sunbeam/local/IGV/igv.sh"
igv_prefs: {ENABLE_ANTIALIASING: true, NAME_PANEL_WIDTH: 360, SAM.MAX_VISIBLE_RANGE: 1000}
keep_unaligned: false
bwa_fp: "/home/zhaoc1/sunbeam/local/bwa"
top_contig: 2
imagemagick_fp: "/home/zhaoc1/sunbeam_neutrino/local/ImageMagick/bin"