Merge pull request #114 from JoseEspinosa/updates

Update paths to test dbs

CHANGELOG.md

@@ -21,7 +21,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #106](https://github.com/nf-core/proteinfold/pull/106) - Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0
 - [PR #108](https://github.com/nf-core/proteinfold/pull/108) - Fix gunzip error when providing too many files when downloading PDBMMCIF database.
 - [PR #111](https://github.com/nf-core/proteinfold/pull/111) - Update pipeline template to [nf-core/tools 2.9](https://github.com/nf-core/tools/releases/tag/2.9).
-- [PR #112](https://github.com/nf-core/rnaseq/pull/112) - Use `nf-validation` plugin for parameter and samplesheet validation
+- [PR #112](https://github.com/nf-core/rnaseq/pull/112) - Use `nf-validation` plugin for parameter and samplesheet validation.
+- [#113](https://github.com/nf-core/proteinfold/pull/113) - Include esmfold dbs for full data sets.
+- [PR #114](https://github.com/nf-core/rnaseq/pull/114) - Update paths to test dbs.
 
 ## 1.0.0 - White Silver Reebok
 

conf/dbs.config

@@ -23,16 +23,16 @@ params {
     uniprot_trembl      = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz'
 
     // Alphafold paths
-    bfd_path               = "${params.alphafold2_db}/bfd/*"
-    small_bfd_path         = "${params.alphafold2_db}/small_bfd/*"
-    alphafold2_params_path = "${params.alphafold2_db}/alphafold_params_*/*"
-    mgnify_path            = "${params.alphafold2_db}/mgnify/*"
-    pdb70_path             = "${params.alphafold2_db}/pdb70/**"
-    pdb_mmcif_path         = "${params.alphafold2_db}/pdb_mmcif/*"
+    bfd_path                 = "${params.alphafold2_db}/bfd/*"
+    small_bfd_path           = "${params.alphafold2_db}/small_bfd/*"
+    alphafold2_params_path   = "${params.alphafold2_db}/alphafold_params_*/*"
+    mgnify_path              = "${params.alphafold2_db}/mgnify/*"
+    pdb70_path               = "${params.alphafold2_db}/pdb70/**"
+    pdb_mmcif_path           = "${params.alphafold2_db}/pdb_mmcif/*"
     uniref30_alphafold2_path = "${params.alphafold2_db}/uniref30/*"
-    uniref90_path          = "${params.alphafold2_db}/uniref90/*"
-    pdb_seqres_path        = "${params.alphafold2_db}/pdb_seqres/*"
-    uniprot_path           = "${params.alphafold2_db}/uniprot/*"
+    uniref90_path            = "${params.alphafold2_db}/uniref90/*"
+    pdb_seqres_path          = "${params.alphafold2_db}/pdb_seqres/*"
+    uniprot_path             = "${params.alphafold2_db}/uniprot/*"
 
     // Colabfold links
     colabfold_db_link       = 'http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz'

conf/test_full.config

@@ -18,5 +18,5 @@ params {
     mode            = 'alphafold2'
     alphafold2_mode = 'standard'
     input           = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
-    alphafold2_db   = 's3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini'
+    alphafold2_db   = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
 }

conf/test_full_alphafold_multimer.config

@@ -19,5 +19,5 @@ params {
     alphafold2_mode         = 'standard'
     alphafold2_model_preset = 'multimer'
     input                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
-    alphafold2_db           = 's3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini'
+    alphafold2_db           = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
 }

conf/test_full_alphafold_split.config

@@ -18,5 +18,5 @@ params {
     mode            = 'alphafold2'
     alphafold2_mode = 'split_msa_prediction'
     input           = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
-    alphafold2_db   = 's3://ngi-igenomes/test-data/proteinfold/db/alphafold_mini'
+    alphafold2_db   = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
 }

conf/test_full_colabfold_local.config

@@ -20,7 +20,7 @@ params {
     colabfold_server        = 'local'
     colabfold_model_preset  = 'alphafold2_ptm'
     input                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
-    colabfold_db            = 's3://ngi-igenomes/test-data/proteinfold/db/colabfold_mini'
+    colabfold_db            = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
 }
 process {
     withName:MMSEQS_COLABFOLDSEARCH {

conf/test_full_colabfold_webserver.config

@@ -19,5 +19,5 @@ params {
     colabfold_server       = 'webserver'
     colabfold_model_preset = 'alphafold2_ptm'
     input                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
-    colabfold_db            = 's3://ngi-igenomes/test-data/proteinfold/db/colabfold_mini'
+    colabfold_db            = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
 }

conf/test_full_colabfold_webserver_multimer.config

@@ -19,5 +19,5 @@ params {
     colabfold_server       = 'webserver'
     colabfold_model_preset = 'alphafold2_multimer_v3'
     input                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
-    colabfold_db           = 's3://ngi-igenomes/test-data/proteinfold/db/colabfold_mini'
+    colabfold_db           = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
 }

conf/test_full_esmfold.config

@@ -18,5 +18,5 @@ params {
     mode                    = 'esmfold'
     esmfold_model_preset    = 'monomer'
     input                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
-    esmfold_db              = 's3://ngi-igenomes/test-data/proteinfold/db/esmfold'
+    esmfold_db              = 's3://proteinfold-dataset/test-data/db/esmfold'
 }

conf/test_full_esmfold_multimer.config

@@ -18,5 +18,5 @@ params {
     mode                    = 'esmfold'
     esmfold_model_preset    = 'multimer'
     input                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
-    esmfold_db              = 's3://ngi-igenomes/test-data/proteinfold/db/esmfold'
+    esmfold_db              = 's3://proteinfold-dataset/test-data/db/esmfold'
 }