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
# 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)
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
project: PathoFact_results
project: Project_A_PathoFact
# 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)
size_fasta: 100000
......@@ -21,32 +17,21 @@ size_fasta: 100000
###########
# Define path to signalP
signalp: "/work/projects/ecosystem_biology/local_tools/SignalP/signalp-4.1/signalp"
signalp: "/path/to/signalp-4.1/signalp"
############
# Toxin #
############
# 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"
database: Toxin
#################
# Virulence #
#################
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 #
......
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