fixed mlst columns

UPHL-BioNGS · Mar 13, 2024 · a91a83e · a91a83e
1 parent 1c08b25
commit a91a83e
Showing 1 changed file with 52 additions and 52 deletions.
diff --git a/bin/summary.py b/bin/summary.py
@@ -562,58 +562,58 @@ def fill_coverage(row):
 
 # reducing to the top 1 or 2 results for each analysis
 final_columns = [
-# general information
-'coverage',
-'per_core_genome_genes',
-'fastqc_total_sequences',
-'fastqc_flagged_sequences',
-'fastqc_avg_length',
-'fastp_passed_reads',
-'bbduk_phix_reads',
-'quast_#_contigs',
-'quast_gc_(%)',
-'warnings',
-'circulocov_unmapped_reads',
-'amrfinder_genes_(per_cov/per_ident)',
-
-# species
-'predicted_organism',
-'mlst_matching_PubMLST_scheme',
-'mlst_ST',
-'fastani_top_organism',
-'fastani_top_reference',
-'fastani_top_ani_estimate',
-'fastani_top_total_query_sequence_fragments',
-'fastani_top_fragments_aligned_as_orthologous_matches',
-'mash_reference',
-'mash_mash-distance',
-'mash_p-value',
-'mash_matching-hashes',
-'mash_organism',
-'plasmidfinder_plasmid_(identity)',
-
-# contamination
-'blobtools_organism_(per_mapped_reads)',
-'kraken2_organism_(per_fragment)',
-
-# species specific information
-'seqsero2_predicted_antigenic_profile',
-'seqsero2_predicted_serotype',
-'emmtyper_predicted_emm-type',
-'kleborate_virulence_score',
-'kleborate_resistance_score',
-'kaptive_best_match_locus_O',
-'kaptive_best_match_locus_K',
-'elgato_st',
-'mykrobe_phylo_group',
-'mykrobe_species',
-'mykrobe_lineage',
-'drprg_susceptibility',
-'pbptyper_pbptype',
-'serotypefinder_Serotype_O',
-'serotypefinder_Serotype_H',
-'shigatyper_prediction',
-'shigatyper_hit']
+    # general information
+    'coverage',
+    'per_core_genome_genes',
+    'fastqc_total_sequences',
+    'fastqc_flagged_sequences',
+    'fastqc_avg_length',
+    'fastp_passed_reads',
+    'bbduk_phix_reads',
+    'quast_#_contigs',
+    'quast_gc_(%)',
+    'warnings',
+    'circulocov_unmapped_reads',
+    'amrfinder_genes_(per_cov/per_ident)',
+
+    # species
+    'predicted_organism',
+    'mlst_matching_pubmlst_scheme',
+    'mlst_st',
+    'fastani_top_organism',
+    'fastani_top_reference',
+    'fastani_top_ani_estimate',
+    'fastani_top_total_query_sequence_fragments',
+    'fastani_top_fragments_aligned_as_orthologous_matches',
+    'mash_reference',
+    'mash_mash-distance',
+    'mash_p-value',
+    'mash_matching-hashes',
+    'mash_organism',
+    'plasmidfinder_plasmid_(identity)',
+
+    # contamination
+    'blobtools_organism_(per_mapped_reads)',
+    'kraken2_organism_(per_fragment)',
+
+    # species specific information
+    'seqsero2_predicted_antigenic_profile',
+    'seqsero2_predicted_serotype',
+    'emmtyper_predicted_emm-type',
+    'kleborate_virulence_score',
+    'kleborate_resistance_score',
+    'kaptive_best_match_locus_O',
+    'kaptive_best_match_locus_K',
+    'elgato_st',
+    'mykrobe_phylo_group',
+    'mykrobe_species',
+    'mykrobe_lineage',
+    'drprg_susceptibility',
+    'pbptyper_pbptype',
+    'serotypefinder_Serotype_O',
+    'serotypefinder_Serotype_H',
+    'shigatyper_prediction',
+    'shigatyper_hit']
 
 set_columns = []
 for new_column in final_columns :