From 04cad9dcd24256d3e5866857049826b7096540b8 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 9 Aug 2024 09:34:32 +1000
Subject: [PATCH] feat(nextflow.config): Added new param variables and defaults
 to the config file

---
 nextflow.config | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index ec71afb5..691ee289 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,48 @@ params {
     full_dbs                    =  false // true full_dbs, false reduced_dbs
     alphafold2_model_preset     = "monomer" // for AF2 {monomer (default), monomer_casp14, monomer_ptm, multimer}
     alphafold2_db               = null
+    
+    // Database prefixes
+    bfd_prefix			= null
+    smallbfd_prefix		= null
+    mgnify_prefix		= null
+    pdb70_prefix		= null
+    pdb_mmcif_prefix		= null
+    uniclust30_prefix		= null
+    uniref90_prefix		= null
+    pdb_seq_prefix		= null
+    uniprot_prefix		= null
+    alphafold_params_prefix	= null
+    mmcif_path			= null
+    mmcif_obsolete		= null
+    uniclust30_db		= null
+    bfd_first_non_consensus_sequences = null
+    uniprot_fasta		= null
+    pdb_seqres_txt		= null
+    bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt = null
+    uniref90_fasta		= null
+    mgy_clusters_fasta		= null
+    uniclust30_prefix		= null
+
+    bfd_name			= null
+    smallbfd_name		= null
+    mgnify_name			= null
+    pdb70_name			= null
+    pdb_mmcif_name		= null
+    uniclust30_name		= null
+    uniref90_name		= null
+    pdb_seqres_name		= null
+    uniprot_name		= null
+    alphafold_params_name	= null
+    mmcif_files_name		= null
+    mmcif_obsolete_name		= null
+    uniclust30_db_name		= null
+    bfd_first_non_consensus_sequences_name = null
+    uniprot_fasta_name		= null
+    pdb_seqres_txt_name		= null
+    bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name = null
+    uniref90_fasta_name		= null
+    mgy_clusters_fasta_name	= null
 
     // Alphafold2 links
     bfd                         = null