projectTitle: "DROP: Detection of RNA Outliers Pipeline"
root: $HOME/project/muscle/FRASER_GETx/Output            # root directory of all output objects and tables
htmlOutputPath: $HOME/project/muscle/FRASER_GETx/Output/html  # path for HTML rendered reports
indexWithFolderName: true # whether the root base name should be part of the index name

hpoFile: $HOME/software/drop_demo/Data/hpo_genes.tsv.gz  # if null, downloads it from webserver
sampleAnnotation: $HOME/project/muscle/FRASER_GETx/sample_annotation.txt # path to sample annotation (see documentation on how to create it)

geneAnnotation:
    v29: $HOME/database/RNA_dia/gencode.v29lift37.annotation.gtf.gz
genomeAssembly: hg19
genome: # path to reference genome sequence in fasta format.
        ucsc: $HOME/database/RNA_dia/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa


exportCounts:
    # specify which gene annotations to include and which
    # groups to exclude when exporting counts
    geneAnnotations:
        - v29

aberrantSplicing:
    run: true
    groups:
        - fraser
    recount: false
    longRead: false
    keepNonStandardChrs: false
    filter: true
    minExpressionInOneSample: 20
    minDeltaPsi: 0.05
    implementation: PCA
    padjCutoff: 1
    zScoreCutoff: 0
    deltaPsiCutoff : 0
    maxTestedDimensionProportion: 6

tools:
    gatkCmd: gatk
    bcftoolsCmd: bcftools
    samtoolsCmd: samtools