fixes after merge

Author: KateSakharova

.github/workflows/nf-test-e2e.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Nextflow 
+      - name: Setup Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "25.10.0"

.github/workflows/nf-test-subwf.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Nextflow 
+      - name: Setup Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "25.10.0"

bin/check_proteins_compatibility.py

@@ -160,7 +160,8 @@ def check_compatibility(fasta: str, proteins_faa: str, proteins_gff: str) -> str
         return NOT_MATCHED
 
     contigs_included = all(
-        any(contig_id in header for header in contig_ids) for contig_id in gff_contig_ids
+        any(contig_id in header for header in contig_ids)
+        for contig_id in gff_contig_ids
     )
     gff_ids_included = all(
         any(protein_id in header for header in faa_headers) for protein_id in gff_ids

nextflow_schema.json

@@ -322,11 +322,11 @@
                     "default": "01-predictions",
                     "description": "output directory for detected viruses step"
                 },
-                "prodigaldir": {
+                "proteindir": {
                     "type": "string",
                     "format": "directory-path",
-                    "default": "02-prodigal",
-                    "description": "output directory for prodigal step"
+                    "default": "02-protein-prediction",
+                    "description": "output directory for protein prediction step"
                 },
                 "hmmerdir": {
                     "type": "string",

subworkflows/local/proteins_compatibility/main.nf

@@ -18,7 +18,7 @@ workflow PROTEINS_COMPATIBILITY {
             def resultsList = results instanceof List ? results : [results]
             tuple(meta, resultsList[0].name)
         }
-    // Check whether a user-supplied fasta/faa/gff triplet is 
+    // Check whether a user-supplied fasta/faa/gff triplet is
     // internally consistent (marked matched or not_matched)
     // and whether the faa/gff still use prodigal's short-format protein IDs and therefore need renaming (marked require_rename)
     checked_records = records_with_proteins

tests/test_data/MGYG000495417_samplesheet.csv

@@ -1,2 +1,2 @@
 id,assembly,proteins_gff,proteins_faa
-MGYG000495417,https://raw.githubusercontent.com/EBI-Metagenomics/emg-viral-pipeline/refs/heads/fix/remove-use-proteins/tests/test_data/MGYG000495417.fna,https://raw.githubusercontent.com/EBI-Metagenomics/emg-viral-pipeline/refs/heads/fix/remove-use-proteins/tests/test_data/MGYG000495417.gff,https://raw.githubusercontent.com/EBI-Metagenomics/emg-viral-pipeline/refs/heads/fix/remove-use-proteins/tests/test_data/MGYG000495417.faa
+MGYG000495417,https://raw.githubusercontent.com/EBI-Metagenomics/emg-viral-pipeline/refs/heads/4.0.0/tests/test_data/MGYG000495417.fna,https://raw.githubusercontent.com/EBI-Metagenomics/emg-viral-pipeline/refs/heads/4.0.0/tests/test_data/MGYG000495417.gff,https://raw.githubusercontent.com/EBI-Metagenomics/emg-viral-pipeline/refs/heads/4.0.0/tests/test_data/MGYG000495417.faa

workflows/virify.nf

@@ -160,7 +160,7 @@ workflow VIRIFY {
         }
 
     SPLIT_PROTEINS(category_fasta.groupTuple().join(protein_files_ch).transpose())
-    
+
     proteins_ch = SPLIT_PROTEINS.out.fasta_proteins_gff
 
     // ----------- ANNOTATE
@@ -197,4 +197,4 @@ workflow VIRIFY {
         false,
         false,
     )
-}
+}