From edff052c835dbd439e16432e0a2ae1ec3b08221d Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 8 Aug 2024 16:07:42 +1000
Subject: [PATCH] feat(run_alphafold2_msa): Removed hardcoded paths and changed
 variables

---
 modules/local/run_alphafold2_msa.nf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index 10d217ca..2e2bbe9b 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -35,13 +35,13 @@ process RUN_ALPHAFOLD2_MSA {
 
     script:
     def args = task.ext.args ?: ''
-    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_variable}bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path=${params.uniclust30_variable}uniclust30_2018_08" :
-        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}bfd-first_non_consensus_sequences.fasta"
+    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${uniclust30_db_name}" :
+        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}${params.bfd_first_non_consensus_sequences_name}"
     if (alphafold2_model_preset == 'multimer') {
-        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_variable}pdb_seqres.txt --uniprot_database_path=${params.uniprot_variable}/uniprot.fasta "
+        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} --uniprot_database_path=${params.uniprot_dir_path}/${params.uniprot_fasta_name} "
     }
     else {
-        alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_variable}pdb70 "
+        alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_dir_path}${params.pdb70_name} "
     }
     """
     #if [ -f pdb_seqres/pdb_seqres.txt ]
@@ -55,8 +55,8 @@ process RUN_ALPHAFOLD2_MSA {
         --db_preset=${db_preset} \
         --output_dir=\$PWD \
         --data_dir=\$PWD \
-        --uniref90_database_path=${params.uniref90_variable}uniref90.fasta \
-        --mgnify_database_path=${params.mgnify_database_path}/mgy_clusters_2022_05.fa \
+        --uniref90_database_path=${params.uniref90_dir_path}/${params.uniref90_fasta_name} \
+        --mgnify_database_path=${params.mgnify_database_path}/${params.mgy_clusters_fasta_name} \
         --template_mmcif_dir=${params.template_mmcif_dir} \
         --obsolete_pdbs_path=${params.obsolete_pdbs_path}  \
         $args