@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix ns1: <https://w3id.org/np/snakemake/> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <https://schema.org/> .
@prefix sub: <https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/> .
@prefix this: <https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU> a np:Nanopublication;
  np:hasAssertion sub:assertion;
  np:hasProvenance sub:provenance;
  np:hasPublicationInfo sub:pubinfo;
  dcterms:created "2026-04-17T13:29:12.172652+00:00"^^xsd:dateTime;
  dcterms:creator orcid:0000-0003-2408-7588;
  npx:hasNanopubType schema:Dataset;
  npx:signedBy orcid:0000-0003-2408-7588;
  rdfs:label "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
  prov:generatedAtTime "2026-04-17T15:29:13.310830"^^xsd:dateTime;
  prov:wasAttributedTo orcid:0000-0003-2408-7588 .

sub: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""" .

sub: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 [https://github.com/gpertea/gffread]. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2].
Next quantification is performed using salmon [https://github.com/COMBINE-lab/salmon] before normalization and differential expression analysis are conducted by PyDESeq2 [https://github.com/owkin/PyDESeq2].
The workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow.
Additionaly, NanoPlot [https://github.com/wdecoster/NanoPlot] is employed to analyze initial sequencing data and QualiMap [https://github.com/EagleGenomics-cookbooks/QualiMap] is used to evaluate mapping results.""";
  ns1:generatedAt "2026-04-17T13:29:12.172652+00:00"^^xsd:dateTime;
  ns1:hasConfigurationSection sub:workflow-configuration .

sub:workflow-configuration rdfs:label "from workflow configuration";
  ns1:hasConfigurationFile sub:config-1 .

sub:assertion prov:generatedAtTime "2026-04-17T15:29:13.310830"^^xsd:dateTime;
  prov:wasAttributedTo orcid:0000-0003-2408-7588 .

sub:sig npx:hasAlgorithm "RSA";
  npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB";
  npx:hasSignature "YKX/2GkgL2KAQ1jHXfHDW511vSbWE34aFAaBQdpQeAZkdVvVnNYVDYiFCHjjb1KuRX2M6DWnOb4PAbZpb8fG8ET+ws6jO4YTKnyGFJZ13tbfB5stXwgfcz53mJ36XYeLvrUuSkmjIUFRkTxZDzKZNCPsloE0STs5tEg9lmqyG0rhEMQhFXONmyd5IOgFCa6r2MMG/NCqhXWxqRP4p5D7dB3RQTJrmwDazF2uZQbtSTPF0Hf0c8BhN8XPO4vABpFVf0R6La5HATARUSSCwIZQLdW6edt6M4Fa0hXGYWQJ9/uslSvDTtWkjJPdeF5OIMFCVEPxBNmJuJ3md23cad5E6g==";
  npx:hasSignatureTarget <https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU>;
  npx:signedBy orcid:0000-0003-2408-7588 .