Commit 39c372a7 authored by Laura Denies's avatar Laura Denies
Browse files

Update config.yaml

parent 5cd7ed8f
# Insert name of input files to run analysis # Insert name of input files to run analysis
# All three input files used by the pipeline for one sample need to be given the same name, followed by the suffix .faa (amino acid, gene fasta file), .fna (nucleotide contig fasta file), .contig (table with contig and gene names). # All three input files used by the pipeline for one sample need to be given the same name, followed by the suffix .faa (amino acid, gene fasta file), .fna (nucleotide contig fasta file), .contig (table with contig and gene names).
# Only give name of files and not the suffix (.faa, .fna, .contig) # Only give name of files and not the suffix (.faa, .fna, .contig)
input_file: ["B4","B12","Mock"] input_file: ["SAMPLE_A","SAMPLE_B"]
#["SRR2005376","SRR2005657","SRR2005659","SRR2005663","SRR2005674","SRR2005698","SRR2005710","SRR2005712","SRR2005719","SRR2005720"]
#["SRR2005676","SRR2005661","SRR2005374","SRR2005707"]
# Define unique name for your project # Define unique name for your project
project: PathoFact_results project: Project_A_PathoFact
# Define dir to files (wil also be the output directory # Define dir to files (wil also be the output directory
OUTDIR: /scratch/users/ldenies/NZ_PathoFact OUTDIR: /path/to/samples
# Define size of split fasta files (default 10 000 sequences/file) # Define size of split fasta files (default 10 000 sequences/file)
size_fasta: 100000 size_fasta: 100000
...@@ -21,32 +17,21 @@ size_fasta: 100000 ...@@ -21,32 +17,21 @@ size_fasta: 100000
########### ###########
# Define path to signalP # Define path to signalP
signalp: "/work/projects/ecosystem_biology/local_tools/SignalP/signalp-4.1/signalp" signalp: "/path/to/signalp-4.1/signalp"
############ ############
# Toxin # # Toxin #
############ ############
# Define path to HMM # Define path to HMM
hmmscan_tool: "/work/projects/ecosystem_biology/local_tools/hmmer-3.2.1/src/hmmsearch" hmmscan_tool: "/path/to/hmmer-3.2.1/src/hmmsearch"
hmm_file: "databases/toxins/combined_Toxin.hmm" hmm_file: "databases/toxins/combined_Toxin.hmm"
database: Toxin
################# #################
# Virulence # # Virulence #
################# #################
vir_hmm_file: "databases/virulence/Virulence_factor.hmm" vir_hmm_file: "databases/virulence/Virulence_factor.hmm"
database_vir: Virulence
threads: 1
########################
# Conda environments #
########################
split_env: "conda_environments/Seqkit.yml"
R_env: "conda_environments/renv.yaml"
############# #############
# AMR # # AMR #
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment