sub1:assertion {
  sub1:config-1 dcterms:identifier "config.yml" ;
    schema:text """samples: samples.csv

ref:
    species: \"Drosophila melanogaster\"
    genome: \"\"
    annotation: \"\"
    accession: \"GCF_000001215.4\"
    ensembl_species: \"\"  # e.g., \"homo_sapiens\"
    build: \"\"  # e.g., \"GRCh38\"
    release: \"\"  # e.g., \"105\"

read_filter:
    min_length: 200

minimap2:
    index_opts: \"\"
    opts: \"\"
    maximum_secondary: 100
    secondary_score_ratio: 1.0

samtools:
    samtobam_opts: \"-b\"
    bamsort_opts: \"\"
    bamindex_opts: \"\"
    bamstats_opts: \"\"

quant:
    salmon_libtype: \"U\"

deseq2:
    fit_type: \"\"
    design_factors:
        - \"condition\"
    lfc_null: 1.0
    alt_hypothesis: \"greaterAbs\"
    point_width: 20
    mincount: 10
    alpha: 0.05
    threshold_plot: 10
    colormap: \"Blues\"
    figtype: \"png\"
    batch_effect:
      - \"\"

isoform_analysis:
    FLAIR: true
    qscore: 1
    exp_thresh: 10
    col_opts: \"--annotation_reliant generate --generate_map --stringent\"

protein_annotation:
    lambda: false
    uniref: \"https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz\"
    num_matches: 3""" .
  sub1:dataset a schema:Dataset ;
    ns1:describesWorkflow "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" ;
    ns1:description """This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology.
First a transcriptome FASTA is constructed using gffread. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2.
Next quantification is performed using salmon before normalization and differential expression analysis are conducted by PyDESeq2.
The workflow can optionally analyze splice-isoforms through integrating the FLAIR workflow.
Additionaly, NanoPlot is employed to analyze initial sequencing data and QualiMap is used to evaluate mapping results.""" ;
    ns1:generatedAt "2026-04-16T15:51:47.211240+00:00"^^xsd:dateTime ;
    ns1:hasConfigurationSection sub1:workflow-configuration .
  sub1:workflow-configuration rdfs:label "from workflow configuration" ;
    ns1:hasConfigurationFile sub1:config-1 .
}