Merge pull request #65 from seqeralabs/seqera-ai/20251128-143953-remove-mmseqs2-add-precomputed-msa

Remove MMSeqs2 and add pre-computed MSA support via samplesheet

Author: FloWuenne

MMSEQS2_MSA_SUMMARY.md

@@ -44,6 +44,10 @@
       "reuse": {
         "type": "boolean",
         "errorMessage": "Reuse must be true or false"
+      },
+      "target_msa": {
+        "type": "string",
+        "errorMessage": "Target MSA must be a valid file path to a pre-computed MSA file (e.g., 'target.a3m' or 'target_msa.fasta')"
       }
     },
     "required": ["sample_id", "design_yaml"]

assets/schema_input_design.json

@@ -1,2 +1,2 @@
-sample_id,design_yaml,structure_files,protocol,num_designs,budget
-2vsm_nanobody_binder,assets/test_data/egfr_nanobody_design.yaml,assets/test_data/2VSM.cif,nanobody-anything,5,2
+sample_id,design_yaml,structure_files,protocol,num_designs,budget,reuse,target_msa
+2vsm_nanobody_binder,assets/test_data/egfr_nanobody_design.yaml,assets/test_data/2VSM.cif,nanobody-anything,5,2,,

assets/test_data/samplesheet_design_nanobody.csv

@@ -1,2 +1,2 @@
-sample_id,design_yaml,structure_files,protocol,num_designs,budget
-2vsm_peptide_binder,assets/test_data/2VSM_peptide_design.yaml,assets/test_data/2VSM.cif,peptide-anything,5,2
+sample_id,design_yaml,structure_files,protocol,num_designs,budget,reuse,target_msa
+2vsm_peptide_binder,assets/test_data/2VSM_peptide_design.yaml,assets/test_data/2VSM.cif,peptide-anything,5,2,,

assets/test_data/samplesheet_design_peptide.csv

@@ -1,2 +1,2 @@
-sample_id,design_yaml,structure_files,protocol,num_designs,budget
-2vsm_protein_binder,assets/test_data/2VSM_protein_design.yaml,assets/test_data/2VSM.cif,protein-anything,5,2
+sample_id,design_yaml,structure_files,protocol,num_designs,budget,reuse,target_msa
+2vsm_protein_binder,assets/test_data/2VSM_protein_design.yaml,assets/test_data/2VSM.cif,protein-anything,5,2,,