@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/RAl-YXmaNyU7wRmmOGrmVugTqHe36Z-txlh4aPXPIeWU8/> .
@prefix this: <https://w3id.org/np/RAl-YXmaNyU7wRmmOGrmVugTqHe36Z-txlh4aPXPIeWU8> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

sub:Head {
  this: a np:Nanopublication;
    np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo .
}

sub:assertion {
  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 "2026-04-17T14:07:59.954639+00:00"^^xsd:dateTime;
    ns1:hasConfigurationSection sub:workflow-configuration .
  
  sub:workflow-configuration rdfs:label "from workflow configuration";
    ns1:hasConfigurationFile sub:config-1 .
}

sub:provenance {
  sub:assertion prov:generatedAtTime "2026-04-17T16:08:02.401532"^^xsd:dateTime;
    prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}

sub:pubinfo {
  this: dcterms:created "2026-04-17T14:07:59.954639+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 "2026-04-17T16:08:02.401532"^^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 "MnZwY2UY0hXpwknx/9zq+JMX5sGjP3cQ+O54k3MwtJwIvs5rivLKybiZBOtHyREfrejXGhE+YfObQtcZWzl6yZVjT5h6V/EE7dVJGvFUAJnexX3Z41JSvMD2bdtGOn+somvIJ3tVAL+Jiw8YF01Zzr/jFZzjfAu32UI/jBABUnbPFlqTknC9KuxWPDw0r0De5UD4Ngn7vX0lioXt84UEPaTUfxcWVcuOUqAnB2cxcwe6gO0m4r06rx7g1k1YB18zUMeUaP1Qn+s+MHAoAOCNn97inTWmbu458xGyaCWjY1EXaaTXveVsAv0AjL5B2vI9FSJqjNF7V6MLZCeRs3LFyg==";
    npx:hasSignatureTarget this:;
    npx:signedBy orcid:0000-0003-2408-7588 .
}