@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 sub1: <http://purl.org/np/RAr5ps2M5JuQSj2nV4TTg8x2Q-1yIBaL30R1xx9vFRqyI#> .
@prefix this: <http://purl.org/np/RAr5ps2M5JuQSj2nV4TTg8x2Q-1yIBaL30R1xx9vFRqyI> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

sub1:Head {
  this: a np:Nanopublication;
    np:hasAssertion sub1:assertion;
    np:hasProvenance sub1:provenance;
    np:hasPublicationInfo sub1:pubinfo .
}

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 .
}

sub1:provenance {
  sub1:assertion prov:generatedAtTime "2026-04-16T17:51:48.644824"^^xsd:dateTime;
    prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}

sub1:pubinfo {
  sub1:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB";
    npx:hasSignature "ZroLEDrlL96XFimrx0ek2T8Cy1ggdRl1wRAl1S+VhtOySlSDO19F9J18Iu/OPBDhjXkf6jhUj2p0/9JdzWll1eQGFFVjNycHrEdlBpGkha4UKrCD3dsaKkpZW0DNn/8CsBduwRbpcUIkZtdIHkF2iKj7RfP5anU5vIrjd6qaOwAoXtVU9sQowlXPYZ1WurZmuz4+H+nAsnJK7nXTwQP3mQu0Ad/NJgQaaz/gBYPXQ1Vf5iJqGbB+G8SmcbO0Hja2d4ng3HjkFWGnhTakIQ9S2gxMZiyiTG/rjQldw2+rTvtwgV6Lr/UCAzv7wGUqJ0azBQfw59UG3lY6J3+cTWCcuQ==";
    npx:hasSignatureTarget this: .
  
  this: dcterms:created "2026-04-16T15:51:47.211240+00:00"^^xsd:dateTime;
    dcterms:creator orcid:0000-0003-2408-7588;
    npx:hasNanopubType schema:Dataset;
    rdfs:label "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
    prov:generatedAtTime "2026-04-16T17:51:48.644824"^^xsd:dateTime;
    prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}