fix

Author: Rachel Colquhoun

bin/type_aas_and_dels.py

@@ -14,7 +14,7 @@ def parse_args():
     parser.add_argument('--reference-fasta', dest = 'reference_fasta', required=True, help='Reference FASTA')
     parser.add_argument('--aas', dest = 'aas', required=False, help='CSV of AAs')
     parser.add_argument('--dels', dest = 'dels', required=False, help='CSV of deletions')
-    paraser.add_argument('--index-column', dest = 'index_column', required=False, default='sequence_name')
+    parser.add_argument('--index-column', dest = 'index_column', required=False, default='sequence_name')
 
     args = parser.parse_args()
     return args

modules/align_and_variant_call_cog_uk.nf

@@ -173,7 +173,8 @@ process uk_type_AAs_and_dels {
       --out-metadata ${uk_metadata.baseName}.typed.csv \
       --reference-fasta ${reference_fasta} \
       --aas ${aas} \
-      --dels ${dels}
+      --dels ${dels} \
+      --index-column query
     """
 }
 

modules/filter_and_trim_cog_uk.nf

@@ -44,7 +44,7 @@ process uk_filter_low_coverage_sequences {
             writer.writeheader()
 
             for row in reader:
-                id = row["fasta_header"]
+                id = row["sequence_name"]
                 if id in alignment:
                     seq = str(alignment[id].seq)
                     mapped_completeness = float(len(seq.replace("N", "")) / len(seq))

modules/publish_all.nf

@@ -29,7 +29,7 @@ process combine_cog_gisaid {
         fastafunk fetch \
           --in-fasta ${uk_fasta} \
           --in-metadata ${uk_metadata} \
-          --index-column fasta_header \
+          --index-column sequence_name \
           --filter-column fasta_header covv_accession_id central_sample_id biosample_source_id secondary_identifier root_sample_id \
                           pillar_2 \
                           sequence_name sample_date epi_week \