bioinfo_config.json

{
    "viralrecon": {
        "mapping_stats": {
            "fn": "mapping_illumina(?:_\\d{8})?\\.tab",
            "sample_col_idx": 2,
            "header_row_idx": 1,
            "required": true,
            "function": null,
            "split_by_batch": true,
            "content": {
                "analysis_date": "analysis_date",
                "depth_of_coverage_value": "medianDPcoveragevirus",
                "number_of_variants_in_consensus": "Variantsinconsensusx10",
                "number_of_variants_with_effect": "MissenseVariants",
                "per_genome_greater_10x": "Coverage>10x(%)",
                "per_Ns": "%Ns10x",
                "per_reads_host": "%readshost",
                "per_reads_virus": "%readsvirus",
                "per_unmapped": "%unmapedreads",
                "qc_filtered": "totalreads",
                "reference_genome_accession": "Virussequence",
                "read_length": "read_length"
            }
        },
        "mapping_pangolin": {
            "fn": ".pangolin(?:.*?)?\\.csv$",
            "header_row_idx": 1,
            "required": false,
            "function": "handle_pangolin_data",
            "extract": true,
            "content": {
                "variant_name": "scorpio_call",
                "lineage_name": "lineage",
                "lineage_algorithm_software_version": "version",
                "lineage_analysis_software_version": "pangolin_version",
                "lineage_analysis_scorpio_version": "scorpio_version",
                "lineage_analysis_constellation_version": "constellation_version",
                "lineage_analysis_date": "lineage_analysis_date",
                "pangolin_database_version": "pangolin_database_version"
            }
        },
        "variants_long_table": {
            "fn": "variants_long_table.csv",
            "sample_col_idx": 1,
            "header_row_idx": 1,
            "required": true,
            "split_by_batch": true,
            "function": "parse_long_table",
            "content": {
                "sample" : "SAMPLE",
                "chromosome": "CHROM",
                "pos": "POS", 
                "alt": "ALT", 
                "ref": "REF",
                "Filter": "FILTER",
                "dp": "DP",
                "ref_dp": "REF_DP",
                "alt_dp": "ALT_DP",
                "af": "AF",
                "effect": "EFFECT",
                "hgvs_c": "HGVS_C",
                "hgvs_p": "HGVS_P",
                "hgvs_p_1_letter": "HGVS_P_1LETTER",
                "caller" : "CALLER",
                "lineage" : "LINEAGE",
                "gene" : "GENE"
            }
        },
        "mapping_consensus": {
            "fn": ".consensus.fa",
            "required": false,
            "function": "handle_consensus_fasta",
            "extract": true,
            "content": {
                "consensus_sequence_name" : "sequence_name",
                "consensus_genome_length" : "genome_length",
                "consensus_sequence_filename" : "sequence_filename",
                "consensus_sequence_filepath" : "sequence_filepath",
                "consensus_sequence_md5" : "sequence_md5", 
                "number_of_base_pairs_sequenced" : "number_of_base_pairs_sequenced"
            }
        },
        "summary_mqc": {
            "fn": "summary_variants_metrics_mqc.csv",
            "sample_col_idx": 1,
            "header_row_idx": 1,
            "required": true,
            "function": null,
            "content": {
                "ns_per_100_kbp": "# Ns per 100kb consensus"
            }
        },
        "other_files": {
            "fn": "^(?!.*tbi$).*.filtered.vcf.gz",
            "required": false,
            "function": null,
            "extract": true,
            "content": {}
        },
        "workflow_summary": {
            "fn": "multiqc_report.html",
            "required": true,
            "function": null,
            "content": {
                "software_version": {
                    "bioinformatics_protocol_software_version": "nf-core/viralrecon",
                    "consensus_sequence_software_version": "bcftools",
                    "dehosting_method_software_version": "kraken2",
                    "mapping_software_version":"bowtie2",
                    "preprocessing_software_version":"fastp",
                    "variant_calling_software_version":"ivar"
                },
                "software_name": {
                    "bioinformatics_protocol_software_name": "nf-core/viralrecon",
                    "consensus_sequence_software_name": "bcftools",
                    "dehosting_method_software_name": "kraken2",
                    "mapping_software_name":"bowtie2",
                    "preprocessing_software_name":"fastp",
                    "variant_calling_software_name":"ivar"
                }
            }
        },
        "fixed_values": {
            "assembly": "Not Provided [GENEPIO:0001668]",
            "assembly_params": "Not Provided [GENEPIO:0001668]",
            "commercial_open_source_both": "Open Source",
            "consensus_params": "-p vcf -f",
            "depth_of_coverage_threshold": ">10x",
            "if_assembly_other": "Not Provided [GENEPIO:0001668]",
            "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]",
            "if_consensus_other": "Not Provided [GENEPIO:0001668]",
            "if_lineage_identification_other": "Not Provided [GENEPIO:0001668]",
            "if_mapping_other": "Not Provided [GENEPIO:0001668]",
            "if_preprocessing_other": "Not Provided [GENEPIO:0001668]",
            "lineage_analysis_software_name": "pangolin",
            "mapping_params": "--seed 1",
            "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred   30    --unqualified_percent_limit 10 --length_required 50",
            "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20   -m10",
            "lineage_analysis_date": "Not Provided [GENEPIO:0001668]"
        }
    }
}