diff --git a/CHANGELOG.md b/CHANGELOG.md index da0a752c..0ec3d617 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/conf/dbs.config b/conf/dbs.config index a9965c52..74398339 100644 --- a/conf/dbs.config +++ b/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' diff --git a/conf/test_full.config b/conf/test_full.config index dc8ff985..2c8a4fae 100644 --- a/conf/test_full.config +++ b/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' } diff --git a/conf/test_full_alphafold_multimer.config b/conf/test_full_alphafold_multimer.config index eca98ba4..2f8b0627 100644 --- a/conf/test_full_alphafold_multimer.config +++ b/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' } diff --git a/conf/test_full_alphafold_split.config b/conf/test_full_alphafold_split.config index b7262d1f..9cb378c2 100644 --- a/conf/test_full_alphafold_split.config +++ b/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' } diff --git a/conf/test_full_colabfold_local.config b/conf/test_full_colabfold_local.config index 44dd270f..90f1c811 100644 --- a/conf/test_full_colabfold_local.config +++ b/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 { diff --git a/conf/test_full_colabfold_webserver.config b/conf/test_full_colabfold_webserver.config index 8c503b09..a9db381a 100644 --- a/conf/test_full_colabfold_webserver.config +++ b/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' } diff --git a/conf/test_full_colabfold_webserver_multimer.config b/conf/test_full_colabfold_webserver_multimer.config index 99063c91..612a1221 100644 --- a/conf/test_full_colabfold_webserver_multimer.config +++ b/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' } diff --git a/conf/test_full_esmfold.config b/conf/test_full_esmfold.config index 8dd8ca74..a3919070 100644 --- a/conf/test_full_esmfold.config +++ b/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' } diff --git a/conf/test_full_esmfold_multimer.config b/conf/test_full_esmfold_multimer.config index 9dc528b3..36445443 100644 --- a/conf/test_full_esmfold_multimer.config +++ b/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' }