Update config.yaml

config.yaml

 # 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    #