output_definition.json

{
    "long_read_rna_pipeline.minimap2": {
        "sam": {
            "path": "minimap2/rep${i+1}/${basename}",
            "table": "Minimap2/Replicate ${i+1}/alignments in sam format"
        },
        "bam": {
            "path": "minimap2/rep${i+1}/${basename}",
            "table": "Minimap2/Replicate ${i+1}/alignments in bam format"
        },
        "log": {
            "path": "minimap2/rep${i+1}/${basename}",
            "table": "Minimap2/Replicate ${i+1}/minimap2 log"
        },
        "mapping_qc": {
            "path": "minimap2/rep${i+1}/${basename}",
            "table": "Minimap2/Replicate ${i+1}/mapping QC"
        }
    },

    "long_read_rna_pipeline.transcriptclean": {
        "corrected_sam": {
            "path": "transcriptclean/rep${i+1}/${basename}",
            "table": "Transcriptclean/Replicate ${i+1}/cleaned sam"
        },
        "corrected_bam": {
            "path": "transcriptclean/rep${i+1}/${basename}",
            "table": "Transcriptclean/Replicate ${i+1}/cleaned bam"
        },
        "corrected_fasta": {
            "path": "transcriptclean/rep${i+1}/${basename}",
            "table": "Transcriptclean/Replicate ${i+1}/cleaned fasta"
        },
        "transcript_log": {
            "path": "transcriptclean/rep${i+1}/${basename}",
            "table": "Transcriptclean/Replicate ${i+1}/transcript log file"
        },
        "transcript_error_log": {
            "path": "transcriptclean/rep${i+1}/${basename}",
            "table": "Transcriptclean/Replicate ${i+1}/Transcript error log file"
        },
        "report": {
            "path": "transcriptclean/rep${i+1}/${basename}",
            "table": "Transcriptclean/Replicate ${i+1}/Transcriptclean report"
        }
    },

    "long_read_rna_pipeline.talon": {
        "talon_config": {
            "path": "talon/rep${i+1}/${basename}",
            "table": "TALON/Replicate ${i+1}/TALON options csv"
        },
        "talon_log": {
            "path": "talon/rep${i+1}/${basename}",
            "table": "TALON/Replicate ${i+1}/TALON log"
        },
        "talon_db_out": {
            "path": "talon/rep${i+1}/${basename}",
            "table": "TALON/Replicate ${i+1}/TALON database"
        }
    },

    "long_read_rna_pipeline.talon_label_reads": {
        "labeled_bam": {
            "path": "talon_label_reads/rep${i+1}/${basename}",
            "table": "TALON_Label_Reads/Replicate ${i+1}/Labeled BAM"
        },
        "labeled_sam": {
            "path": "talon_label_reads/rep${i+1}/${basename}",
            "table": "TALON_Label_Reads/Replicate ${i+1}/Labeled SAM"
        },
        "read_labels_tsv": {
            "path": "talon_label_reads/rep${i+1}/${basename}",
            "table": "TALON_Label_Reads/Replicate ${i+1}/Read label TSV"
        }
    },

    "long_read_rna_pipeline.create_abundance_from_talon_db": {
        "talon_abundance": {
            "path": "create_abundance_from_talon_db/rep${i+1}/${basename}",
            "table": "Create_Abundance_from_TALON/Replicate ${i+1}/abundance .tsv"
        },
        "number_of_genes_detected": {
            "path": "create_abundance_from_talon_db/rep${i+1}/${basename}",
            "table": "Create_Abundance_from_TALON/Replicate ${i+1}/number of genes detected"
        }
    },

    "long_read_rna_pipeline.create_gtf_from_talon_db": {
        "gtf": {
            "path": "create_gtf_from_talon_db/rep${i+1}/${basename}",
            "table": "Create_GTF_from_TALON/Replicate ${i+1}/gtf from updated TALON db"
        }
    },

    "long_read_rna_pipeline.calculate_spearman": {
        "spearman": {
            "path": "calculate_spearman/${basename}",
            "table": "Spearman/replicates spearman correlation"
        }
    }
}