feat(run_alphafold2): Changed hardcoded paths to use variables and up…

…dated variable names
Australian-Structural-Biology-Computing · Aug 8, 2024 · c218ad2 · c218ad2
1 parent 2a79fe4
commit c218ad2
Showing 1 changed file with 12 additions and 10 deletions.
diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf
@@ -34,28 +34,30 @@ process RUN_ALPHAFOLD2 {
 
     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/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}${params.uniclust30_db_name}" :
+        "reduced_dbs --small_bfd_database_path=${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=${params.pdb_dir_path}${params.pdb70_name} "
     }
     """
-    if [ -f ${params.pdb_seqres_variable}pdb_seqres.txt ]
-        then sed -i "/^\\w*0/d" ${params.pdb_seqres_variable}pdb_seqres.txt
+    if [ -f ${params.pdb_seqres_dir_path}/${params.pbd_seqres_txt_name} ]
+        \$PDB_SEQRES_TEMP=\$(mktemp --directory)
+        cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
+        then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}
     fi
-    if [ -d params/alphafold_params_* ]; then ln -r -s params/alphafold_params_*/* params/; fi
+    if [ -d ${params.alphafold2_params_path} ]; then ln -r -s ${params.alphafold2_params_path} params/; fi
     python3 /app/alphafold/run_alphafold.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \
         --db_preset=${db_preset} \
         --output_dir=\$PWD \
         --data_dir=\$PWD \
-        --uniref90_database_path=${params.uniref90_variable}uniref90.fasta \
-        --template_mmcif_dir=${params.pdb_mmcif_variable}mmcif_files \
-        --obsolete_pdbs_path=${params.pdb_mmcif_variable}obsolete.dat \
+        --uniref90_database_path=${params.uniref90_dir_path}uniref90.fasta \
+        --template_mmcif_dir=${params.template_mmcif_dir} \
+        --obsolete_pdbs_path=${params.obsolete_pdbs_path} \
         --random_seed=53343 \
         $args