Missing fields when read-bioinfo-metadata is executed

[Shettland]

I've noticed that not all the fields are correctly incorporated into the json file when executing read-bioinfo-metadata module. I'd expect this behaviour when there were anything wrong, but the report shown via prompt does not show any error in the process.

Some of the missing fields that I've found that were not pointed out in the report:

• [x] 'bioinformatics_protocol_software_name',
• [x] 'bioinformatics_protocol_software_version',
• [x] 'consensus_genome_length',
• [x] 'consensus_sequence_filename',
• [x] 'consensus_sequence_filepath',
• [x] 'consensus_sequence_md5',
• [x] 'consensus_sequence_name',
• [x] 'consensus_sequence_software_version',
• [x] 'dehosting_method_software_version',
• [x] 'depth_of_coverage_value',
• [x] 'lineage_algorithm_software_version',
• [x] 'lineage_analysis_constellation_version',
• [x] 'lineage_analysis_scorpio_version',
• [x] 'lineage_analysis_software_version',
• [x] 'lineage_name',
• [x] 'mapping_software_version',
• [x] 'ns_per_100_kbp',
• [x] 'number_of_base_pairs_sequenced',
• [x] 'number_of_variants_in_consensus',
• [x] 'number_of_variants_with_effect',
• [x] 'per_Ns',
• [x] 'per_genome_greater_10x',
• [x] 'per_reads_host',
• [x] 'per_reads_virus',
• [x] 'per_unmapped',
• [x] 'preprocessing_software_version',
• [x] 'qc_filtered',
• [x] 'read_length',
• [x] 'reference_genome_accession',
• [x] 'variant_calling_software_name',
• [x] 'variant_calling_software_version',
• [x] 'variant_name'