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      "@value" : "## General Workflow Parameters:\n\n# sample information and experimental design\nsamples: samples.csv\n\n## Workflow-specific Parameters:\n# Define reference genome/transcriptome\nref:\n    species: \"Drosophila melanogaster\"\n    # Local reference data\n    # Genome file path (supported extensions: .fa, .fna, .fasta, case-insensitive)\n    # may be a path or left empty, if download using an accession number is preferred\n    genome: \"\"\n    # Annotation file (supported extensions: .gff, .gtf, case-insensitive)\n    # may be a path or left empty, if download using an accession number is preferred\n    annotation: \"\"\n    # Remote reference data\n    # NCBI accession number of the reference data set; can be left empty if both reference files are available locally\"\n    #accession: \"GCF_000001215.2\"\n    accession: \"GCF_000001215.4\"\n    ensembl_species: \"\"  # e.g., \"homo_sapiens\"\n    build: \"\"  # e.g., \"GRCh38\"\n    release: \"\"  # e.g., \"105\"\n\nread_filter:\n    # Minimum read length; set 0 to keep all reads.\n    min_length: 200\n\n# minimap2 alignment parameters\nminimap2:\n    # Minimap2 indexing options\n    index_opts: \"\"\n    # Minimap2 mapping options\n    opts: \"\"\n    # Maximum secondary alignments\n    maximum_secondary: 100\n    # Secondary score ratio (-p for minimap2)\n    secondary_score_ratio: 1.0\n\n# samtools processing parameters\nsamtools:\n    # Samtools view opts, \"-b\" creates BAM from SAM.\n    samtobam_opts: \"-b\"\n    # Samtools sort opts,\n    bamsort_opts: \"\"\n    # Samtools index opts,\n    bamindex_opts: \"\"\n    # Samtools stats opts\n    bamstats_opts: \"\"\n\n# salmon quantification parameters\nquant:\n    # Salmon library type (Default: U)\n    salmon_libtype: \"U\"\n\n# This section defines the pyDESeq2 plot and data handling parameters\ndeseq2:\n    # normalization fit type, must be 'parametric' or 'mean'\n    fit_type: \"\"\n    # the \"design factors\" are the confounding variables to be adjusted for\n    # during normalization. They must be given in the configuration (samples.csv).\n    design_factors:\n        - \"condition\"\n    #\n    # the \"continuous factors\" are non-categorial factors to be considered\n    #continuous_factors:\n    #    -\n    #\n    # The (log2) log fold change under the null hypothesis. (default: 0).\n    lfc_null: 1.0\n    #\n    # The alternative hypothesis for computing wald p-values. By default,\n    # the normal Wald test assesses deviation of the estimated log fold\n    # change from the null hypothesis, as given by lfc_null.\n    # One of [\"greaterAbs\", \"lessAbs\", \"greater\", \"less\"] or None.\n    # The alternative hypothesis corresponds to what the user wants to\n    # find rather than the null hypothesis. (default: None).\n    alt_hypothesis: \"greaterAbs\"\n    #\n    # The marker size in points**2 (typographic points are 1/72 in.).\n    # Default is rcParams['lines.markersize'] ** 2.# minimum count to\n    # be considered for subsequent analysis\n    point_width: 20\n    #\n    # we disregard loci with count number lower 'mincount'\n    mincount: 10\n    #\n    # Type I error cutoff value:\n    alpha: 0.05\n    #\n    # in addition to the full heatmap, plot the top number of different\n    # values, ranked by the top ratio between the two traits\n    threshold_plot: 10\n    #\n    # the heatmap color map\n    # see https://seaborn.pydata.org/tutorial/color_palettes.htm for an overview\n    colormap: \"Blues\"\n    #plot figure type\n    figtype: \"png\"\n    batch_effect: \n      - \"\"\n    #\n## Differential Isoform Analysis\n\n# The FLAIR splice-isoform analysis pipeline includes resource-intensive computations and only works with additional constraints.\n#     1. In 'samples.csv: The 'condition' column must contain exactly two distinct values. For example 'control' and 'treated'.\n#     2. In 'samples.csv: Refrain from using underscores when naming samples. The 'sample' column may contain underscores, but be aware that underscores will be removed from the name for isoform quantification steps.\n#     3. In this file: the variable 'FLAIR' below must be:'true'. This is a check to determine if users are aware of the constraints and wish to proceed.\nisoform_analysis:\n    # Enables FLAIR Isoform Analysis if 'true'\n    FLAIR: true\n    # Minimum MAPQ of read assignment to an isoform (default: 1).\n    qscore: 1\n    # min read count expression threshold. 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