Updated pathing

Australian-Structural-Biology-Computing · Nov 15, 2024 · b78cdee · b78cdee
1 parent 8cc32e1
commit b78cdee
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Showing 2 changed files with 3 additions and 16 deletions.
diff --git a/conf/dbs.config b/conf/dbs.config
@@ -49,26 +49,14 @@ params {
     ]
 
     // RoseTTAFold links
-	uniref30              = 'http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz'
+    uniref30              = 'http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz'
     pdb100                = 'https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz'
 
     // RoseTTAFold paths
     uniref30_rosettafold_all_atom_path  = "${params.rosettafold_all_atom_db}/uniref30/UniRef30_2020_06/*"
     pdb100_path                         = "${params.rosettafold_all_atom_db}/pdb100_2021Mar03/*"
     bfd_rosettafold_all_atom_path       = "${params.rosettafold_all_atom_db}/bfd/*"
 
-    // Helixfold3 links
-    uniclust30_link             = 'https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz'
-    ccd_preprocessed_link       = 'https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz'
-    rfam_link                   = 'https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta'
-    helixfold3_init_models_link = 'https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip'
-
-    // Helixfold3 paths
-    uniclust30_path             = "${params.helixfold3_db}/uniclust30/*"
-    ccd_preprocessed_path       = "${params.helixfold3_db}/ccd_preprocessed_etkdg.pkl.gz"
-    rfam_path                   = "${params.helixfold3_db}/Rfam-14.9_rep_seq.fasta"
-    helixfold3_init_models_path = "${params.helixfold3_db}"
-
     // Esmfold links
     esmfold_3B_v1                        = 'https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt'
     esm2_t36_3B_UR50D                    = 'https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt'

diff --git a/modules/local/run_rosettafold_all_atom.nf b/modules/local/run_rosettafold_all_atom.nf
@@ -1,5 +1,5 @@
 /*
- * Run RoseTTAFold_All_Atom 
+ * Run RoseTTAFold_All_Atom
  */
 process RUN_ROSETTAFOLD_ALL_ATOM {
     tag "$meta.id"
@@ -18,7 +18,7 @@ process RUN_ROSETTAFOLD_ALL_ATOM {
     path ('bfd/*')
     path ('UniRef30_2020_06/*')
     path ('pdb100_2021Mar03/*')
-    
+
     output:
     path ("${fasta.baseName}*")
     tuple val(meta), path ("${meta.id}_rosettafold_all_atom.pdb")   , emit: main_pdb
@@ -34,7 +34,6 @@ process RUN_ROSETTAFOLD_ALL_ATOM {
     ln -s /app/RoseTTAFold-All-Atom/* .
 
     mamba run --name RFAA python -m rf2aa.run_inference \
-    loader_params.MAXCYCLE=1 \
     checkpoint_path="/srv/scratch/sbf/rfaa/RFAA_paper_weights.pt" \
     --config-dir /app/RoseTTAFold-All-Atom/rf2aa/config/inference \
     --config-name "${fasta}"