Merge pull request nf-core#315 from tlitfin-unsw/add-db-flag

Add global db flag

Author: JoseEspinosa

CHANGELOG.md

@@ -40,6 +40,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #306](https://github.com/nf-core/proteinfold/pull/306)] - extract_output.py -> extract_metrics.py so pLDDT, MSA, PAE emitted as raw data .tsv files
 - [[PR #307](https://github.com/nf-core/proteinfold/pull/307)] - Update Boltz-1 boilerplate and formatting.
 - [[PR #314](https://github.com/nf-core/proteinfold/pull/314)] - Fix extract metrics for broken modules.
+- [[PR #315](https://github.com/nf-core/proteinfold/pull/315)] - Add global db flag.
+- [[#263](https://github.com/nf-core/proteinfold/issues/263)] - Removed broken colabfold options (`auto` and `alphafold2`)
 - [[PR #316](https://github.com/nf-core/proteinfold/pull/316)] - Add process_gpu label to modules which use GPU.
 
 ### Parameters

nextflow.config

@@ -14,6 +14,7 @@ params {
     mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, helixfold3, boltz}
     use_gpu                     = false
     split_fasta                 = false
+    db                          = null
 
     // Alphafold2 parameters
     alphafold2_mode             = "standard"
@@ -62,7 +63,7 @@ params {
 
     // Colabfold parameters
     colabfold_server            = "webserver"
-    colabfold_model_preset      = "alphafold2_ptm" // {'auto', 'alphafold2', 'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'}
+    colabfold_model_preset      = "alphafold2_ptm" // {'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'}
     num_recycles_colabfold      = 3
     use_amber                   = true
     colabfold_db                = null
@@ -147,16 +148,6 @@ params {
     helixfold3_obsolete_path            = null
     helixfold3_maxit_src_path           = null
 
-    // Boltz links
-    boltz_ccd_link           = null
-    boltz_model_link         = null
-
-    // Boltz parameters and paths
-    boltz_db                    = null
-    boltz_ccd_path              = null
-    boltz_model_path            = null
-    boltz_use_msa_server        = false
-
     // Foldseek params
     foldseek_search = null
     foldseek_easysearch_arg = null
@@ -471,6 +462,21 @@ validation {
     }
 }
 
+if (params.mode.toLowerCase().split(",").contains("alphafold2"))
+    { params.alphafold2_db = params.alphafold2_db ?: params.db }
+if (params.mode.toLowerCase().split(",").contains("colabfold"))
+    { params.colabfold_db = params.colabfold_db ?: params.db }
+if (params.mode.toLowerCase().split(",").contains("esmfold"))
+    { params.esmfold_db = params.esmfold_db ?: params.db }
+if (params.mode.toLowerCase().split(",").contains("rosettafold_all_atom"))
+    { params.rosettafold_all_atom_db = params.rosettafold_all_atom_db ?: params.db }
+if (params.mode.toLowerCase().split(",").contains("helixfold3"))
+    { params.helixfold3_db = params.helixfold3_db ?: params.db }
+if (params.mode.toLowerCase().split(",").contains("boltz")) {
+    params.boltz_db = params.boltz_db ?: params.db
+    params.colabfold_db = params.colabfold_db ?: params.db
+}
+
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'