Merge pull request #159 from JoseEspinosa/updates

Update magnify paths
nf-core · Jun 3, 2024 · d33e481 · d33e481
2 parents 4308842 + b9e4c13
commit d33e481
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diff --git a/docs/usage.md b/docs/usage.md
@@ -68,7 +68,7 @@ If you specify the `--alphafold2_db ` parameter, the directory structure of your
 
 ```
 ├── mgnify
-│   └── mgy_clusters_2018_12.fa
+│   └── mgy_clusters_2022_05.fa
 ├── alphafold_params_2022-03-02
 │   ├── LICENSE
 │   ├── params_model_1_multimer.npz

diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf
@@ -57,7 +57,7 @@ process RUN_ALPHAFOLD2 {
         --output_dir=\$PWD \
         --data_dir=\$PWD \
         --uniref90_database_path=./uniref90/uniref90.fasta \
-        --mgnify_database_path=./mgnify/mgy_clusters_2018_12.fa \
+        --mgnify_database_path=./mgnify/mgy_clusters_2022_05.fa \
         --template_mmcif_dir=./pdb_mmcif/mmcif_files \
         --obsolete_pdbs_path=./pdb_mmcif/obsolete.dat \
         --random_seed=53343 \

diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
@@ -56,7 +56,7 @@ process RUN_ALPHAFOLD2_MSA {
         --output_dir=\$PWD \
         --data_dir=\$PWD \
         --uniref90_database_path=./uniref90/uniref90.fasta \
-        --mgnify_database_path=./mgnify/mgy_clusters_2018_12.fa \
+        --mgnify_database_path=./mgnify/mgy_clusters_2022_05.fa \
         --template_mmcif_dir=./pdb_mmcif/mmcif_files \
         --obsolete_pdbs_path=./pdb_mmcif/obsolete.dat  \
         $args