@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix orcid: <https://orcid.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix schema: <http://schema.org/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcmitype: <http://purl.org/dc/dcmitype/> .

orcid:0000-0003-2408-7588 foaf:name "Christian Meesters", "Christian Meesters";
  <http://www.wikidata.org/entity/P1344> <https://w3id.org/spaces/nanopub/nanosessions/session32>,
    <https://w3id.org/spaces/nanopub/nanosessions/session31>, <https://w3id.org/spaces/nanopub/nanosessions/session30>,
    <https://w3id.org/spaces/nanopub/nanosessions/session29>, <https://w3id.org/spaces/nanopub/nanosessions/session28>,
    <https://w3id.org/spaces/nanopub/nanosessions/session27>, <https://w3id.org/spaces/nanopub/nanosessions/session26>,
    <https://w3id.org/np/RA1EqFlHdJgd4CTdfRP8XrWDFsVrSHsuXk362eb924i5M/GlobalOSRetreat>;
  <http://purl.org/petapico/o/paperclub#hasRead> <https://doi.org/10.37044/osf.io/7whtf>,
    <https://doi.org/10.26434/chemrxiv.15000200/v1>, <https://doi.org/10.12688/f1000research.29032.3>;
  <https://w3id.org/kpxl/gen/terms/plansToAttend> <https://w3id.org/spaces/nanopub/nanosessions/session32>,
    <https://w3id.org/spaces/nanopub/nanosessions/session31>, <https://w3id.org/spaces/nanopub/nanosessions/session30>;
  npx:approvesOf <https://w3id.org/np/RA47-3RJKZ2rjQd3_UWsPKohSdLzNlaUPTWFRZi2MmxlY>,
    <https://w3id.org/np/RAqeFWDFgwiOk1EidDSEklc1dLrDDWFL6hN5B-nPS7QCA>, <https://w3id.org/np/RAQcw-nCBs-TtaAxoJHgGhK6m_gBmQsA1XKY-cfA502ac> .

<https://w3id.org/np/RALGjMHt8qoFP8EyHLWctpRwZZbQjVrKiw_NvADWC3nUc#M..yTtRc..> npx:declaredBy
    orcid:0000-0003-2408-7588;
  npx:hasAlgorithm "RSA";
  npx:hasKeyLocation <https://nanodash.petapico.org/>;
  npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCKyTtRc5W2LD8SIQhd+T7IOhgr4GinEVpynNUiUppNi1Yvdo+qHljDplzsXlxc4pPwEB2+/RBYT75rMeD/VrV12s5Aq9t5XalDFKnxPE1vFN4P3dINAOq8ikc1yzU0fpJpz09+tefHG+Zk1Mz90PnLWLCs30wM6Iq6hI5NHmjklQIDAQAB" .

<https://w3id.org/np/RA7A14becTEH4iLYvyPMEvY8K1K2ck4o6SW-pgDaH6wuE#M..DVJTS..> npx:declaredBy
    orcid:0000-0003-2408-7588;
  npx:hasAlgorithm "RSA";
  npx:hasKeyLocation <https://nanodash.knowledgepixels.com/>;
  npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQC+DVJTSCzdJUJMzlwRfb2Qm2NZpuZ932RpVliWxMAhmZ6ZkeeibmJlW/Z0q51YkFArJIWbJ0f7rLQWM5epuZV4I5cjMqepOWGey6LrPolMs8lI9dJf9zW9lJsneV+py3U8WsrB6mg//pkEeXnVDd+WscADyXJ5EeLwoZjCkPn8/QIDAQAB" .

<https://doi.org/10.5281/zenodo.19734951> rdfs:label "OSPARK output - Managing Outreach on Open Research Material to Heterogeneous Groups" .

<https://w3id.org/np/RAxi5mJwS-F0iSUJ73x_mL_WPMo3piv5FX44Ll9t2Bnu4/readaction> a schema:ReadAction;
  schema:agent orcid:0000-0003-2408-7588;
  schema:endTime "2026-05-29";
  schema:object <https://doi.org/10.5281/zenodo.19734951>;
  rdfs:comment "How to best manage Open Research / Science material to heterogeneous groups is an open challenge. Particularly, as there is a lot of resistance to overcome." .

<https://doi.org/10.37044/osf.io/7whtf> rdfs:comment "I am a sceptic of web applications and reproducibility. However, knowing some participants of this hackathon personally, I gained some trust." .

<https://doi.org/10.26434/chemrxiv.15000200/v1> rdfs:comment "interesting summary for ligand screening and validation" .

<https://doi.org/10.12688/f1000research.29032.3> rdfs:comment "corner stone of data analysis" .

<https://w3id.org/np/RASupe59FA10izXlZT9lXo72q8o7I9qMGkWIKJayNIDBk/SnakemakeSoftwareProvenance>
  a <http://www.wikidata.org/entity/Q604733>;
  dct:date "2026-06-09"^^<http://www.w3.org/2001/XMLSchema#date>;
  dct:description """This presentation is a first version towards better software provenance using the Snakemake workflow management system. It shows the use and benefits of a plugin which stores software metadata using Nanopublication.

The uploaded version is the one I wanted to show - actually, due to a computer crash an abridged, makeshift version was shown. Additional slides let see, where I did a live demonstration.""";
  rdfs:label "Software provenance with Snakemake";
  rdfs:seeAlso <https://doi.org/10.5281/zenodo.21159947>;
  <http://www.wikidata.org/entity/P823> orcid:0000-0003-2408-7588;
  <https://schema.org/about> <http://www.wikidata.org/entity/Q1425625> .

<https://w3id.org/np/RAsl3P0Rn_Mpj9k4zhTixr4AV9jRrZkNpUcbTbSnBTZ94/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RAwFcjl5bJueJ0y43ywSlqCeBeXjZEEsM94DuubcZ8dMU/past-events-view> .

<https://w3id.org/np/RAm8KFHmfnHXr0vpu4lcj3W8D5bfoYcBAQTA72KiwGjlI/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RAAv1iftC6WJiEEbJgPjqhxQEpL7GbVx9ccipVDJZJOAc/user-posts-view> .

<https://w3id.org/np/RAMGiNN_w_gHsY6LRbq63zj9IVh9cC9cw3-PzK8z5EeZc/assertion> rdfs:label
    "@Tobias actually, we already did start an introductory slide set. See the first link.";
  rdfs:seeAlso <https://w3id.org/np/RAKpq1VEaJnWDwNpf4mSSX4NbIERUbE8Kz1VUGQ4PniZ0>,
    <https://w3id.org/np/RAz25iqVXH4PWBENKSqdUBAif3oDVgUa2-GVU30HD1lLE>;
  <https://schema.org/about> <https://w3id.org/spaces/nanopub/nanosessions/session32> .

<https://w3id.org/np/RA3HtVACkBn4Yrqd-v2hpoctpKpIaldjjUAb_2dxcVn9w/assertion> rdfs:label
    "@Daniel I opened a GitHub issue regarding missing licensing information when using the nanopub python library. (see first link)";
  rdfs:seeAlso <https://github.com/Nanopublication/nanopub-py/issues/231>, <https://w3id.org/np/RAc4fE4k3Uz5H0nwjfRiNjWAAYdeZRfmotHibkpAMnijQ>;
  <https://schema.org/about> <https://w3id.org/spaces/nanopub/nanosessions/session32> .

<https://w3id.org/np/RACk_gOf859PDtZqIf3OuCk7bxlqmgxv5--cEKvj5t2Fc/assertion> rdfs:label
    """@Daniel Yes, Snakemake can containerize entire workflows (the linked docs only speak of dockerization, but Apptainer is supported too - since the last hackathon).

Container are, in turn, one of three ways to provide software (Conda, HPC module files and Apptainer).""";
  rdfs:seeAlso <https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#containerization-of-conda-based-workflows>,
    <https://w3id.org/np/RAL1PHq3-MznUphJM36iMArLkIRMYntaG_qMpS0F4iNhc>;
  <https://schema.org/about> <https://w3id.org/spaces/nanopub/nanosessions/session32> .

<https://w3id.org/np/RA_rmYS_m2EUGnE4yk91H15FW0sSCpV_c_tAuN4v04Tuc/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RA6xFOn_39usF8UTpeURiv9_8KYCDuv22XDUykvyQ7mH8/queries-by-user-view> .

<https://w3id.org/np/RAPUabHBmuVF4aJaH-926jcmwaO2ybczd8cRsmeEe0cKg/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RAOw_wkO7C8lKpG7ZXsAXtVk6VFH9kV8CaCqyz-WBhM5U/templates-by-user-view> .

<https://w3id.org/np/RAq26GSbRVMwQ32kmTFh4Fmf3dNR6g86ZnfP_tV-L4ERU> rdfs:comment "Thank you! Daniel & me had a nice discussion. Eventually, I will answer the remaining questions as verbosely as possible per nanopubs, too." .

<https://w3id.org/np/RAO1y_pJSgOXU_UYKoSzaPgJ-ZVmLcRjAR1A7AAyW1Dgo/assertion> rdfs:label
    "What is this space about?";
  <https://schema.org/about> <https://w3id.org/fair/3pff/FA.10.T.1> .

<https://w3id.org/np/RAkj5lwBpJVQVT2qqrsKvxXDQ0acotxRsgXpOSLBv04_E/How_many_nanopubs_to_a_journal_article?>
  a <https://www.wikidata.org/entity/Q189756>;
  rdfs:label """How many nanopubs to a journal article? That would be an interesting statistical question over time. A bit of meta-science. Perhaps something to stratify over research areas as nanopubs are for everyone.

Anyone interested?""" .

<https://w3id.org/np/RA8rPcBcreaZF01eA6Xeh_wwqQcM-Nz7xQyKbLhRHkCXA/SnamakeReportRegistrations>
  a <https://w3id.org/kpxl/grlc/grlc-query>;
  dct:description "Will list all Snakemake report registrations created by this template: https://w3id.org/np/RAsmNjwvzjYfc8Hson0gyjSL6Oov3nZZEfRy7TOFtO5I8 - will need update if the template updates.";
  dct:license <http://www.apache.org/licenses/LICENSE-2.0>;
  rdfs:label "Snakemake Report Registrations";
  <https://w3id.org/kpxl/grlc/endpoint> <https://w3id.org/np/l/nanopub-query-1.1/repo/full>;
  <https://w3id.org/kpxl/grlc/sparql> """PREFIX np:  <http://www.nanopub.org/nschema#>
PREFIX npa: <http://purl.org/nanopub/admin/>
PREFIX npx: <http://purl.org/nanopub/x/>
PREFIX dct: <http://purl.org/dc/terms/>

SELECT DISTINCT ?np ?date
WHERE {
  # any triple (any graph) where the template appears as object
  ?np ?p <https://w3id.org/np/RAsmNjwvzjYfc8Hson0gyjSL6Oov3nZZEfRy7TOFtO5I8> .
  # get its creation date (admin graph)
  GRAPH npa:graph { ?np dct:created ?date }
}
LIMIT 100""" .

<https://w3id.org/np/RApMWbZ0ixGj88tPB4cEamKJQuQTZ5Dxpjh1a5BWteTdE/SnakemakeWorkflowRegistrations>
  a <https://w3id.org/kpxl/grlc/grlc-query>;
  dct:description "Will return all workflow registered with https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk - might need updates from time to time.";
  dct:license <http://www.apache.org/licenses/LICENSE-2.0>;
  rdfs:label "Snakemake Workflow Registrations";
  <https://w3id.org/kpxl/grlc/endpoint> <https://w3id.org/np/l/nanopub-query-1.1/repo/full>;
  <https://w3id.org/kpxl/grlc/sparql> """PREFIX np:  <http://www.nanopub.org/nschema#>
PREFIX npa: <http://purl.org/nanopub/admin/>
PREFIX npx: <http://purl.org/nanopub/x/>
PREFIX dct: <http://purl.org/dc/terms/>

SELECT DISTINCT ?np ?date
WHERE {
  # any triple (any graph) where the template appears as object
  ?np ?p <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk> .
  # get its creation date (admin graph)
  GRAPH npa:graph { ?np dct:created ?date }
}
LIMIT 100""" .

<https://w3id.org/np/RAzeQbv1gXqKIuLic4xTP1gYRnL4YhU_5oRl62nbNl2Xk/SakemakeTerm> a
    <https://w3id.org/kpxl/grlc/grlc-query>;
  dct:description "lists all nanopubs mentioning the Snakemake Workflow Management System";
  dct:license <http://www.apache.org/licenses/LICENSE-2.0>;
  rdfs:label "Snakemake Mentionings";
  <https://w3id.org/kpxl/grlc/endpoint> <https://w3id.org/np/l/nanopub-query-1.1/repo/full>;
  <https://w3id.org/kpxl/grlc/sparql> """PREFIX np: <http://www.nanopub.org/nschema#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX npa: <http://purl.org/nanopub/admin/>
PREFIX npx: <http://purl.org/nanopub/x/>
prefix kpxl: <https://w3id.org/kpxl/gen/terms/>
SELECT DISTINCT ?np ?assertion ?p ?o 
WHERE {
  ?np a np:Nanopublication ;
      np:hasAssertion ?assertion .

  GRAPH ?assertion {
    ?s ?p ?o .

    FILTER (
      isLiteral(?o) &&
      REGEX(STR(?o), \"snakemake\", \"i\")
    )
  }
}

#LIMIT 100""" .

<https://w3id.org/np/RAZHJmoLraSc7aDip-wMlArYrUWivp5XWHtppVyHYhTgM> rdfs:comment """We have the nanopub tutorial page: https://nanopub.net/docs/tutorials/

And this gentle intro: https://saranjeetkaur.github.io/nanopub_101/#/title-slide also expressed as fair training material: https://w3id.org/np/RAz25iqVXH4PWBENKSqdUBAif3oDVgUa2-GVU30HD1lLE - and probably other resources.""" .

<https://w3id.org/np/RAXccBCQpMGFBcWUT5yQZ2kAN-n4fMipbbg-sc9XeRWjc/assertion> rdfs:comment
    """To be able to put a label on these kind of computational tasks will become increasingly important.

To measure it, is perhaps not easy, but feasible.

To weight it in terms of costs and benefits (e.g. through avoiding other computational tasks such as re-computing/re-searching other peoples results) is virtually impossible.""" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/config-1> dct:identifier
    "config.yml";
  <https://schema.org/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""" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/dataset> a <https://schema.org/Dataset>;
  <https://w3id.org/np/snakemake/describesWorkflow> "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
  <https://w3id.org/np/snakemake/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.""";
  <https://w3id.org/np/snakemake/generatedAt> "2026-05-05T18:00:57.134252+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>;
  <https://w3id.org/np/snakemake/hasConfigurationSection> <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/workflow-configuration>;
  <https://w3id.org/np/snakemake/hasRuleSection> <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/workflow-rules> .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-alignment_qa>
  <https://w3id.org/np/snakemake/hasInput> "sorted_alignments/{sample}_sorted.bam";
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/{sample}";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/qualimap/bamqc/environment.yaml@v4.4.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-alignment_qa_report>
  <https://w3id.org/np/snakemake/hasInput> "QC/qualimap/{sample}";
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/{sample}/qualimapReport.html";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_index>
  <https://w3id.org/np/snakemake/hasInput> "sorted_alignments/{sample}_sorted.bam";
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/{sample}_sorted.bam.bai";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/index/environment.yaml@v7.6.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_sort>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.bam";
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/{sample}_sorted.bam";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/sort/environment.yaml@v7.6.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_stats>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.bam";
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/{sample}.txt";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/stats/environment.yaml@v3.13.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_to_bed>
  <https://w3id.org/np/snakemake/hasInput> "sorted_alignments/{sample}_sorted.bam",
    "sorted_alignments/{sample}_sorted.bam.bai";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/beds/{sample}.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-build_flair_genome_index>
  <https://w3id.org/np/snakemake/hasInput> "references/genomic.fa";
  <https://w3id.org/np/snakemake/hasOutput> "index/flair_genome_index.mmi";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-build_minimap_index>
  <https://w3id.org/np/snakemake/hasInput> "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "index/transcriptome_index.mmi";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-concatenate_beds>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/beds/barcode10.bed", "iso_analysis/beds/barcode11.bed",
    "iso_analysis/beds/barcode12.bed", "iso_analysis/beds/barcode13.bed", "iso_analysis/beds/barcode15.bed",
    "iso_analysis/beds/barcode16.bed";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/beds/all_samples.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-correct_transcriptome>
  <https://w3id.org/np/snakemake/hasInput> "transcriptome/transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "gffread>=0.12.7" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-count_reads>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.bam", "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "counts/{sample}_salmon/quant.sf";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "salmon>=1.10.3" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-deseq2> <https://w3id.org/np/snakemake/hasInput>
    "de_analysis/all.rds";
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/{factor}_{prop_a}_vs_{prop_b}_MA_plot.svg",
    "de_analysis/{factor}_{prop_a}_vs_{prop_b}_count_heatmap.svg", "de_analysis/{factor}_{prop_a}_vs_{prop_b}_dispersion_plot.svg",
    "de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv", "de_analysis/{factor}_{prop_a}_vs_{prop_b}_sample_heatmap.svg",
    "de_analysis/{factor}_{prop_a}_vs_{prop_b}_top_count_heatmap.svg";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "bioconductor-deseq2 =1.46.0",
    "r-ashr =2.2_63", "r-pheatmap", "r-rcolorbrewer", "r-stringr =1.5.1" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-deseq2_init>
  <https://w3id.org/np/snakemake/hasInput> "/fshpc/meesters/projects/snakemake-workflows/rna-longseq-de-isoform/config/demo/samples.csv",
    "merged/all_counts_gene.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/all.rds", "de_analysis/normcounts.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "bioconductor-deseq2 =1.46.0",
    "r-ashr =2.2_63", "r-pheatmap", "r-rcolorbrewer", "r-stringr =1.5.1" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ensembl_annotation>
  <https://w3id.org/np/snakemake/hasOutput> "references/ensembl_annotation.gff3";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-annotation/environment.yaml@v7.5.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ensembl_genome>
  <https://w3id.org/np/snakemake/hasOutput> "references/ensembl_genome.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-sequence/environment.yaml@v7.5.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ncbi_annotation>
  <https://w3id.org/np/snakemake/hasOutput> "references/ncbi_dataset_annotation.zip";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "ncbi-datasets-cli>=18.14.0", "unzip>=6.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ncbi_genome>
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  <https://w3id.org/np/snakemake/hasSoftwarePackage> "ncbi-datasets-cli>=18.14.0", "unzip>=6.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-filter_reads>
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  <https://w3id.org/np/snakemake/hasSoftwarePackage> "biopython >=1.84", "pandas>=2.2.2",
    "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_align>
  <https://w3id.org/np/snakemake/hasInput> "filter/barcode10_filtered.fq", "filter/barcode11_filtered.fq",
    "filter/barcode12_filtered.fq", "filter/barcode13_filtered.fq", "filter/barcode15_filtered.fq",
    "filter/barcode16_filtered.fq", "index/flair_genome_index.mmi", "references/genomic.fa";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/align/flair.bam", "iso_analysis/align/flair.bam.bai",
    "iso_analysis/align/flair.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_collapse>
  <https://w3id.org/np/snakemake/hasInput> "filter/barcode10_filtered.fq", "filter/barcode11_filtered.fq",
    "filter/barcode12_filtered.fq", "filter/barcode13_filtered.fq", "filter/barcode15_filtered.fq",
    "filter/barcode16_filtered.fq", "iso_analysis/align/flair_all_corrected.bed", "references/genomic.fa",
    "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/collapse/flair.isoforms.bed",
    "iso_analysis/collapse/flair.isoforms.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_correct>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/align/flair.bed", "references/genomic.fa",
    "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/align/flair_all_corrected.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_diffexp>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/diffexp/genes_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf",
    "iso_analysis/diffexp/genes_deseq2_{condition_value1}_v_{condition_value2}.tsv", "iso_analysis/diffexp/isoforms_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf",
    "iso_analysis/diffexp/isoforms_deseq2_{condition_value1}_v_{condition_value2}.tsv",
    "iso_analysis/diffexp/isoforms_drimseq_{condition_value1}_v_{condition_value2}.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_plot_isoforms>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/collapse/flair.isoforms.bed",
    "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/plots";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_quantify>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/collapse/flair.isoforms.bed",
    "iso_analysis/collapse/flair.isoforms.fa", "iso_analysis/reads_manifest.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "flair=2.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-generate_gene_query>
  <https://w3id.org/np/snakemake/hasInput> "de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv",
    "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "biopython >=1.84", "pandas>=2.2.2",
    "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-genome_to_transcriptome>
  <https://w3id.org/np/snakemake/hasInput> "references/genomic.fa", "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.fa.fai", "transcriptome/transcriptome.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "gffread>=0.12.7" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_annotation>
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.gff";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "ncbi-datasets-cli>=18.14.0", "unzip>=6.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_genome>
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "ncbi-datasets-cli>=18.14.0", "unzip>=6.0.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_indexed_protein_db>
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/index/UniRef.lba.gz";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "wget>=1.21.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_protein_names>
  <https://w3id.org/np/snakemake/hasInput> "protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8";
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/proteins_{factor}_{prop_a}_vs_{prop_b}.csv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "biopython >=1.84", "pandas>=2.2.2",
    "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-gff_to_gtf>
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  <https://w3id.org/np/snakemake/hasOutput> "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "gffread>=0.12.7" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-iso_analysis_report>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/plots";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/report/isoforms", "iso_analysis/report/usage";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-lambda_gene_annotation>
  <https://w3id.org/np/snakemake/hasInput> "protein_annotation/index/UniRef.lba.gz",
    "protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa";
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "lambda>=3.1.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-map_reads>
  <https://w3id.org/np/snakemake/hasInput> "filter/{sample}_filtered.fq", "index/transcriptome_index.mmi";
  <https://w3id.org/np/snakemake/hasOutput> "alignments/{sample}.sam";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/minimap2/aligner/environment.yaml@v7.6.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-merge_read_counts>
  <https://w3id.org/np/snakemake/hasInput> "counts/barcode10_salmon/quant.sf", "counts/barcode11_salmon/quant.sf",
    "counts/barcode12_salmon/quant.sf", "counts/barcode13_salmon/quant.sf", "counts/barcode15_salmon/quant.sf",
    "counts/barcode16_salmon/quant.sf";
  <https://w3id.org/np/snakemake/hasOutput> "merged/all_counts.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "pandas>=2.2.2", "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-pca> <https://w3id.org/np/snakemake/hasInput>
    "de_analysis/all.rds";
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/pca_{variable}.svg";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "bioconductor-deseq2 =1.46.0",
    "r-ashr =2.2_63", "r-pheatmap", "r-rcolorbrewer", "r-stringr =1.5.1" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-reads_manifest>
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/reads_manifest.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "pandas>=2.2.2", "python>=3.12.4" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-sam_to_bam>
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  <https://w3id.org/np/snakemake/hasOutput> "alignments/{sample}.bam";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/view/environment.yaml@v7.6.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-sample_qa_plot>
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  <https://w3id.org/np/snakemake/hasSoftwarePackage> "nanoplot" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-standardize_gff>
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  <https://w3id.org/np/snakemake/hasOutput> "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "agat>=1.4.0" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-total_sample_qa_plot>
  <https://w3id.org/np/snakemake/hasInput> "/lustre/project/nhr-zdvhpc/dtest/raw/barcode10.fastq.gz",
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    "/lustre/project/nhr-zdvhpc/dtest/raw/barcode13.fastq.gz", "/lustre/project/nhr-zdvhpc/dtest/raw/barcode15.fastq.gz",
    "/lustre/project/nhr-zdvhpc/dtest/raw/barcode16.fastq.gz";
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "nanoplot" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-transcriptid_to_gene>
  <https://w3id.org/np/snakemake/hasInput> "merged/all_counts.tsv", "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasOutput> "merged/all_counts_gene.tsv", "merged/transcriptid_to_gene_plot.svg";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "anndata=0.10.8", "bioinfokit",
    "pydeseq2=0.4.10", "seaborn>=0.13.2" .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/workflow-configuration>
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  <https://w3id.org/np/snakemake/hasConfigurationFile> <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/config-1> .

<https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/workflow-rules>
  rdfs:label "workflow rules";
  <https://w3id.org/np/snakemake/hasWorkflowRule> <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-alignment_qa>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-alignment_qa_report>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_index>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_sort>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_stats>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-bam_to_bed>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-build_flair_genome_index>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-build_minimap_index>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-concatenate_beds>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-correct_transcriptome>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-count_reads>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-deseq2>, <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-deseq2_init>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ensembl_annotation>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ensembl_genome>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ncbi_annotation>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-download_ncbi_genome>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-filter_reads>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_align>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_collapse>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_correct>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_diffexp>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_plot_isoforms>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-flair_quantify>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-generate_gene_query>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-genome_to_transcriptome>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_annotation>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_genome>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_indexed_protein_db>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-get_protein_names>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-gff_to_gtf>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-iso_analysis_report>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-lambda_gene_annotation>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-map_reads>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-merge_read_counts>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-pca>, <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-reads_manifest>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-sam_to_bam>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-sample_qa_plot>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-standardize_gff>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-total_sample_qa_plot>,
    <https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g/rule-transcriptid_to_gene> .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/config-1> dct:identifier
    "config.yml";
  <https://schema.org/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""" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/dataset> a <https://schema.org/Dataset>;
  <https://w3id.org/np/snakemake/describesWorkflow> "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
  <https://w3id.org/np/snakemake/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.""";
  <https://w3id.org/np/snakemake/generatedAt> "2026-05-05T15:42:06.149516+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>;
  <https://w3id.org/np/snakemake/hasConfigurationSection> <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/workflow-configuration>;
  <https://w3id.org/np/snakemake/hasRuleSection> <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/workflow-rules> .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-alignment_qa>
  <https://w3id.org/np/snakemake/hasInput> "sorted_alignments/{sample}_sorted.bam";
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/{sample}";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/qualimap/bamqc/environment.yaml@v4.4.0",
    "v4.4.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-alignment_qa_report>
  <https://w3id.org/np/snakemake/hasInput> "QC/qualimap/{sample}";
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/{sample}/qualimapReport.html";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/base.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_index>
  <https://w3id.org/np/snakemake/hasInput> "sorted_alignments/{sample}_sorted.bam";
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/{sample}_sorted.bam.bai";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/index/environment.yaml@v7.6.0",
    "v7.6.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_sort>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.bam";
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/{sample}_sorted.bam";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/sort/environment.yaml@v7.6.0",
    "v7.6.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_stats>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.bam";
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/{sample}.txt";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/stats/environment.yaml@v3.13.4",
    "v3.13.4" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_to_bed>
  <https://w3id.org/np/snakemake/hasInput> "sorted_alignments/{sample}_sorted.bam",
    "sorted_alignments/{sample}_sorted.bam.bai";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/beds/{sample}.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-build_flair_genome_index>
  <https://w3id.org/np/snakemake/hasInput> "references/genomic.fa";
  <https://w3id.org/np/snakemake/hasOutput> "index/flair_genome_index.mmi";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0",
    "v7.6.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-build_minimap_index>
  <https://w3id.org/np/snakemake/hasInput> "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "index/transcriptome_index.mmi";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0",
    "v7.6.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-concatenate_beds>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/beds/barcode10.bed", "iso_analysis/beds/barcode11.bed",
    "iso_analysis/beds/barcode12.bed", "iso_analysis/beds/barcode13.bed", "iso_analysis/beds/barcode15.bed",
    "iso_analysis/beds/barcode16.bed";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/beds/all_samples.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/base.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-correct_transcriptome>
  <https://w3id.org/np/snakemake/hasInput> "transcriptome/transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/gffread.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-count_reads>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.bam", "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "counts/{sample}_salmon/quant.sf";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/salmon.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-deseq2> <https://w3id.org/np/snakemake/hasInput>
    "de_analysis/all.rds";
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/{factor}_{prop_a}_vs_{prop_b}_MA_plot.svg",
    "de_analysis/{factor}_{prop_a}_vs_{prop_b}_count_heatmap.svg", "de_analysis/{factor}_{prop_a}_vs_{prop_b}_dispersion_plot.svg",
    "de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv", "de_analysis/{factor}_{prop_a}_vs_{prop_b}_sample_heatmap.svg",
    "de_analysis/{factor}_{prop_a}_vs_{prop_b}_top_count_heatmap.svg";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/deseq2.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-deseq2_init>
  <https://w3id.org/np/snakemake/hasInput> "/fshpc/meesters/projects/snakemake-workflows/rna-longseq-de-isoform/config/demo/samples.csv",
    "merged/all_counts_gene.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/all.rds", "de_analysis/normcounts.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/deseq2.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ensembl_annotation>
  <https://w3id.org/np/snakemake/hasOutput> "references/ensembl_annotation.gff3";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-annotation/environment.yaml@v7.5.0",
    "v7.5.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ensembl_genome>
  <https://w3id.org/np/snakemake/hasOutput> "references/ensembl_genome.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-sequence/environment.yaml@v7.5.0",
    "v7.5.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ncbi_annotation>
  <https://w3id.org/np/snakemake/hasOutput> "references/ncbi_dataset_annotation.zip";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/reference.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ncbi_genome>
  <https://w3id.org/np/snakemake/hasOutput> "references/ncbi_dataset_genome.zip";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/reference.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-filter_reads>
  <https://w3id.org/np/snakemake/hasInput> "<function <lambda> at 0x7fcf6a1dce00>";
  <https://w3id.org/np/snakemake/hasOutput> "filter/{sample}_filtered.fq";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/biopython.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_align>
  <https://w3id.org/np/snakemake/hasInput> "filter/barcode10_filtered.fq", "filter/barcode11_filtered.fq",
    "filter/barcode12_filtered.fq", "filter/barcode13_filtered.fq", "filter/barcode15_filtered.fq",
    "filter/barcode16_filtered.fq", "index/flair_genome_index.mmi", "references/genomic.fa";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/align/flair.bam", "iso_analysis/align/flair.bam.bai",
    "iso_analysis/align/flair.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_collapse>
  <https://w3id.org/np/snakemake/hasInput> "filter/barcode10_filtered.fq", "filter/barcode11_filtered.fq",
    "filter/barcode12_filtered.fq", "filter/barcode13_filtered.fq", "filter/barcode15_filtered.fq",
    "filter/barcode16_filtered.fq", "iso_analysis/align/flair_all_corrected.bed", "references/genomic.fa",
    "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/collapse/flair.isoforms.bed",
    "iso_analysis/collapse/flair.isoforms.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_correct>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/align/flair.bed", "references/genomic.fa",
    "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/align/flair_all_corrected.bed";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_diffexp>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/diffexp/genes_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf",
    "iso_analysis/diffexp/genes_deseq2_{condition_value1}_v_{condition_value2}.tsv", "iso_analysis/diffexp/isoforms_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf",
    "iso_analysis/diffexp/isoforms_deseq2_{condition_value1}_v_{condition_value2}.tsv",
    "iso_analysis/diffexp/isoforms_drimseq_{condition_value1}_v_{condition_value2}.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_plot_isoforms>
  <https://w3id.org/np/snakemake/hasInput> "<function <lambda> at 0x7fcf6a1df2e0>",
    "iso_analysis/collapse/flair.isoforms.bed", "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/plots";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_quantify>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/collapse/flair.isoforms.bed",
    "iso_analysis/collapse/flair.isoforms.fa", "iso_analysis/reads_manifest.tsv";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/flair.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-generate_gene_query>
  <https://w3id.org/np/snakemake/hasInput> "de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv",
    "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/biopython.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-genome_to_transcriptome>
  <https://w3id.org/np/snakemake/hasInput> "references/genomic.fa", "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.fa.fai", "transcriptome/transcriptome.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/gffread.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_annotation>
  <https://w3id.org/np/snakemake/hasInput> "<function <lambda> at 0x7fcf6a394cc0>";
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.gff";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/reference.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_genome>
  <https://w3id.org/np/snakemake/hasInput> "<function <lambda> at 0x7fcf6a394d60>";
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.fa";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/reference.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_indexed_protein_db>
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/index/UniRef.lba.gz";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/wget.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_protein_names>
  <https://w3id.org/np/snakemake/hasInput> "protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8";
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/proteins_{factor}_{prop_a}_vs_{prop_b}.csv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/biopython.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-gff_to_gtf>
  <https://w3id.org/np/snakemake/hasInput> "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasOutput> "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/gffread.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-iso_analysis_report>
  <https://w3id.org/np/snakemake/hasInput> "iso_analysis/plots";
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/report/isoforms", "iso_analysis/report/usage";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/base.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-lambda_gene_annotation>
  <https://w3id.org/np/snakemake/hasInput> "protein_annotation/index/UniRef.lba.gz",
    "protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa";
  <https://w3id.org/np/snakemake/hasOutput> "protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/lambda3.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-map_reads>
  <https://w3id.org/np/snakemake/hasInput> "filter/{sample}_filtered.fq", "index/transcriptome_index.mmi";
  <https://w3id.org/np/snakemake/hasOutput> "alignments/{sample}.sam";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/minimap2/aligner/environment.yaml@v7.6.0",
    "v7.6.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-merge_read_counts>
  <https://w3id.org/np/snakemake/hasInput> "counts/barcode10_salmon/quant.sf", "counts/barcode11_salmon/quant.sf",
    "counts/barcode12_salmon/quant.sf", "counts/barcode13_salmon/quant.sf", "counts/barcode15_salmon/quant.sf",
    "counts/barcode16_salmon/quant.sf";
  <https://w3id.org/np/snakemake/hasOutput> "merged/all_counts.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/pandas.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-pca> <https://w3id.org/np/snakemake/hasInput>
    "de_analysis/all.rds";
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/pca_{variable}.svg";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/deseq2.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-reads_manifest>
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/reads_manifest.tsv";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/pandas.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-sam_to_bam>
  <https://w3id.org/np/snakemake/hasInput> "alignments/{sample}.sam";
  <https://w3id.org/np/snakemake/hasOutput> "alignments/{sample}.bam";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "github.com/snakemake/snakemake-wrappers/bio/samtools/view/environment.yaml@v7.6.0",
    "v7.6.0" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-sample_qa_plot>
  <https://w3id.org/np/snakemake/hasInput> "<function <lambda> at 0x7fcf6a397ba0>";
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/{sample}/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/nanoplot.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-standardize_gff>
  <https://w3id.org/np/snakemake/hasInput> "references/genomic.gff";
  <https://w3id.org/np/snakemake/hasOutput> "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/agat.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-total_sample_qa_plot>
  <https://w3id.org/np/snakemake/hasInput> "/lustre/project/nhr-zdvhpc/dtest/raw/barcode10.fastq.gz",
    "/lustre/project/nhr-zdvhpc/dtest/raw/barcode11.fastq.gz", "/lustre/project/nhr-zdvhpc/dtest/raw/barcode12.fastq.gz",
    "/lustre/project/nhr-zdvhpc/dtest/raw/barcode13.fastq.gz", "/lustre/project/nhr-zdvhpc/dtest/raw/barcode15.fastq.gz",
    "/lustre/project/nhr-zdvhpc/dtest/raw/barcode16.fastq.gz";
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/nanoplot.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-transcriptid_to_gene>
  <https://w3id.org/np/snakemake/hasInput> "merged/all_counts.tsv", "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/hasOutput> "merged/all_counts_gene.tsv", "merged/transcriptid_to_gene_plot.svg";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "../envs/pydeseq2.yml" .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/workflow-configuration>
  rdfs:label "from workflow configuration";
  <https://w3id.org/np/snakemake/hasConfigurationFile> <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/config-1> .

<https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/workflow-rules>
  rdfs:label "workflow rules";
  <https://w3id.org/np/snakemake/hasWorkflowRule> <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-alignment_qa>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-alignment_qa_report>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_index>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_sort>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_stats>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-bam_to_bed>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-build_flair_genome_index>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-build_minimap_index>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-concatenate_beds>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-correct_transcriptome>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-count_reads>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-deseq2>, <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-deseq2_init>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ensembl_annotation>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ensembl_genome>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ncbi_annotation>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ncbi_genome>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-filter_reads>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_align>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_collapse>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_correct>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_diffexp>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_plot_isoforms>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-flair_quantify>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-generate_gene_query>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-genome_to_transcriptome>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_annotation>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_genome>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_indexed_protein_db>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-get_protein_names>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-gff_to_gtf>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-iso_analysis_report>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-lambda_gene_annotation>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-map_reads>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-merge_read_counts>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-pca>, <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-reads_manifest>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-sam_to_bam>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-sample_qa_plot>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-standardize_gff>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-total_sample_qa_plot>,
    <https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-transcriptid_to_gene> .

<https://w3id.org/np/RAADaVktkG0gDOwhf46WfzYVQvEPznOslI5evR9D3rZd8/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RAPzA6INPpTqOfq6Q7UX2owT-RTLapITvrCIk-D-rSs-U/coauthors-view> .

<https://doi.org/10.37044/osf.io/h6zqj_v2> a <http://purl.org/spar/fabio/ScholarlyWork>;
  <http://purl.org/spar/cito/citesAsAuthority> <https://doi.org/10.12688/f1000research.29032.3>,
    <https://doi.org/10.7717/peerj-cs.1159>;
  <http://purl.org/spar/cito/citesAsDataSource> <https://doi.org/10.5281/ZENODO.19684066>;
  <http://purl.org/spar/cito/citesAsRecommendedReading> <https://doi.org/10.12688/f1000research.29032.3>,
    <https://doi.org/10.53962/hm1w-cg>;
  <http://purl.org/spar/cito/usesMethodIn> <https://doi.org/10.1007/978-3-642-18638-7_6>,
    <https://doi.org/10.1186/s13059-019-1891-0> .

<https://w3id.org/spaces/biohackathon-europe/2026> <https://w3id.org/kpxl/gen/terms/hasObserver>
    orcid:0000-0003-2408-7588 .

<https://saranjeetkaur.github.io/nanopub_101/> a <https://w3id.org/fair/connect/FAIR-Training-Material>;
  dct:MediaType <https://w3id.org/np/RAz25iqVXH4PWBENKSqdUBAif3oDVgUa2-GVU30HD1lLE/html>;
  dct:creator <https://w3id.org/np/RAz25iqVXH4PWBENKSqdUBAif3oDVgUa2-GVU30HD1lLE/0000-0002-7038-1457>,
    <https://w3id.org/np/RAz25iqVXH4PWBENKSqdUBAif3oDVgUa2-GVU30HD1lLE/0000-0003-2408-7588>;
  rdfs:comment "A gentle introduction to Nanopubs";
  rdfs:label "Nanopub 101";
  rdfs:seeAlso <https://github.com/SaranjeetKaur/nanopub_101/>;
  skos:related <http://edamontology.org/topic_0219>, <http://purl.obolibrary.org/obo/NCIT_C142491> .

<https://w3id.org/np/RAzX7hDm_uDpJ4JJOl5nQU4CVfuGkP-vqonvyHQPzJjMw/assertion> rdfs:comment
    "Welcome!" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/config-1> dct:identifier
    "config.yml";
  <https://schema.org/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""" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/dataset> a <https://schema.org/Dataset>;
  <https://w3id.org/np/snakemake/describesWorkflow> "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
  <https://w3id.org/np/snakemake/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.""";
  <https://w3id.org/np/snakemake/generatedAt> "2026-04-17T15:19:46.851430+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>;
  <https://w3id.org/np/snakemake/hasConfigurationSection> <https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/workflow-configuration> .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-1-alignment_qa>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/barcode10";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-10-alignment_qa_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/barcode13/qualimapReport.html";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-11-alignment_qa_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/barcode15/qualimapReport.html";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-12-alignment_qa_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/barcode16/qualimapReport.html";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-13-bam_sort>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/barcode10_sorted.bam";
  <https://w3id.org/np/snakemake/ruleName> "bam_sort" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-14-bam_sort>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/barcode11_sorted.bam";
  <https://w3id.org/np/snakemake/ruleName> "bam_sort" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-15-bam_sort>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/barcode12_sorted.bam";
  <https://w3id.org/np/snakemake/ruleName> "bam_sort" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-16-bam_sort>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/barcode13_sorted.bam";
  <https://w3id.org/np/snakemake/ruleName> "bam_sort" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-17-bam_sort>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/barcode15_sorted.bam";
  <https://w3id.org/np/snakemake/ruleName> "bam_sort" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-18-bam_sort>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_alignments/barcode16_sorted.bam";
  <https://w3id.org/np/snakemake/ruleName> "bam_sort" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-19-bam_stats>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/barcode10.txt";
  <https://w3id.org/np/snakemake/ruleName> "bam_stats" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-2-alignment_qa>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/barcode11";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-20-bam_stats>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/barcode11.txt";
  <https://w3id.org/np/snakemake/ruleName> "bam_stats" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-21-bam_stats>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/barcode12.txt";
  <https://w3id.org/np/snakemake/ruleName> "bam_stats" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-22-bam_stats>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/barcode13.txt";
  <https://w3id.org/np/snakemake/ruleName> "bam_stats" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-23-bam_stats>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/barcode15.txt";
  <https://w3id.org/np/snakemake/ruleName> "bam_stats" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-24-bam_stats>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/bamstats/barcode16.txt";
  <https://w3id.org/np/snakemake/ruleName> "bam_stats" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-25-build_flair_genome_index>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "index/flair_genome_index.mmi";
  <https://w3id.org/np/snakemake/ruleName> "build_flair_genome_index" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-26-build_minimap_index>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "index/transcriptome_index.mmi";
  <https://w3id.org/np/snakemake/ruleName> "build_minimap_index" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-27-correct_transcriptome>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "transcriptome/corrected_transcriptome.fa";
  <https://w3id.org/np/snakemake/ruleName> "correct_transcriptome" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-28-count_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "counts/barcode10_salmon/quant.sf";
  <https://w3id.org/np/snakemake/ruleName> "count_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-29-count_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "counts/barcode11_salmon/quant.sf";
  <https://w3id.org/np/snakemake/ruleName> "count_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-3-alignment_qa>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/barcode12";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-30-count_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "counts/barcode12_salmon/quant.sf";
  <https://w3id.org/np/snakemake/ruleName> "count_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-31-count_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "counts/barcode13_salmon/quant.sf";
  <https://w3id.org/np/snakemake/ruleName> "count_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-32-count_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "counts/barcode15_salmon/quant.sf";
  <https://w3id.org/np/snakemake/ruleName> "count_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-33-count_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "counts/barcode16_salmon/quant.sf";
  <https://w3id.org/np/snakemake/ruleName> "count_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-34-deseq2>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/condition_wt_vs_mt_MA_plot.svg",
    "de_analysis/condition_wt_vs_mt_count_heatmap.svg", "de_analysis/condition_wt_vs_mt_dispersion_plot.svg",
    "de_analysis/condition_wt_vs_mt_l2fc.tsv", "de_analysis/condition_wt_vs_mt_sample_heatmap.svg",
    "de_analysis/condition_wt_vs_mt_top_count_heatmap.svg";
  <https://w3id.org/np/snakemake/ruleName> "deseq2" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-35-deseq2_init>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "de_analysis/all.rds", "de_analysis/normcounts.tsv";
  <https://w3id.org/np/snakemake/ruleName> "deseq2_init" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-36-download_ncbi_annotation>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/ncbi_dataset_annotation.zip";
  <https://w3id.org/np/snakemake/ruleName> "download_ncbi_annotation" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-37-download_ncbi_genome>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/ncbi_dataset_genome.zip";
  <https://w3id.org/np/snakemake/ruleName> "download_ncbi_genome" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-38-filter_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "filter/barcode10_filtered.fq";
  <https://w3id.org/np/snakemake/ruleName> "filter_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-39-filter_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "filter/barcode11_filtered.fq";
  <https://w3id.org/np/snakemake/ruleName> "filter_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-4-alignment_qa>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/barcode13";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-40-filter_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "filter/barcode12_filtered.fq";
  <https://w3id.org/np/snakemake/ruleName> "filter_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-41-filter_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "filter/barcode13_filtered.fq";
  <https://w3id.org/np/snakemake/ruleName> "filter_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-42-filter_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "filter/barcode15_filtered.fq";
  <https://w3id.org/np/snakemake/ruleName> "filter_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-43-filter_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "filter/barcode16_filtered.fq";
  <https://w3id.org/np/snakemake/ruleName> "filter_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-44-flair_align>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/align/flair.bam", "iso_analysis/align/flair.bam.bai",
    "iso_analysis/align/flair.bed";
  <https://w3id.org/np/snakemake/ruleName> "flair_align" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-45-flair_collapse>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/collapse/flair.isoforms.bed",
    "iso_analysis/collapse/flair.isoforms.fa";
  <https://w3id.org/np/snakemake/ruleName> "flair_collapse" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-46-flair_correct>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/align/flair_all_corrected.bed";
  <https://w3id.org/np/snakemake/ruleName> "flair_correct" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-47-flair_diffexp>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/diffexp/genes_deseq2_QCplots_wt_v_mt.pdf",
    "iso_analysis/diffexp/genes_deseq2_wt_v_mt.tsv", "iso_analysis/diffexp/isoforms_deseq2_QCplots_wt_v_mt.pdf",
    "iso_analysis/diffexp/isoforms_deseq2_wt_v_mt.tsv", "iso_analysis/diffexp/isoforms_drimseq_wt_v_mt.tsv";
  <https://w3id.org/np/snakemake/ruleName> "flair_diffexp" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-48-flair_plot_isoforms>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/plots";
  <https://w3id.org/np/snakemake/ruleName> "flair_plot_isoforms" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-49-flair_quantify>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/quantify/flair.counts.tsv";
  <https://w3id.org/np/snakemake/ruleName> "flair_quantify" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-5-alignment_qa>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/barcode15";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-50-genome_to_transcriptome>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.fa.fai", "transcriptome/transcriptome.fa";
  <https://w3id.org/np/snakemake/ruleName> "genome_to_transcriptome" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-51-get_annotation>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.gff";
  <https://w3id.org/np/snakemake/ruleName> "get_annotation" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-52-get_genome>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/genomic.fa";
  <https://w3id.org/np/snakemake/ruleName> "get_genome" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-53-gff_to_gtf>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/standardized_genomic.gtf";
  <https://w3id.org/np/snakemake/ruleName> "gff_to_gtf" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-54-iso_analysis_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/report/isoforms", "iso_analysis/report/usage";
  <https://w3id.org/np/snakemake/ruleName> "iso_analysis_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-55-map_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode10.sam";
  <https://w3id.org/np/snakemake/ruleName> "map_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-56-map_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode11.sam";
  <https://w3id.org/np/snakemake/ruleName> "map_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-57-map_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode12.sam";
  <https://w3id.org/np/snakemake/ruleName> "map_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-58-map_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode13.sam";
  <https://w3id.org/np/snakemake/ruleName> "map_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-59-map_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode15.sam";
  <https://w3id.org/np/snakemake/ruleName> "map_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-6-alignment_qa>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "QC/qualimap/barcode16";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-60-map_reads>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode16.sam";
  <https://w3id.org/np/snakemake/ruleName> "map_reads" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-61-merge_read_counts>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "merged/all_counts.tsv";
  <https://w3id.org/np/snakemake/ruleName> "merge_read_counts" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-62-reads_manifest>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "iso_analysis/reads_manifest.tsv";
  <https://w3id.org/np/snakemake/ruleName> "reads_manifest" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-63-sam_to_bam>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode10.bam";
  <https://w3id.org/np/snakemake/ruleName> "sam_to_bam" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-64-sam_to_bam>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode11.bam";
  <https://w3id.org/np/snakemake/ruleName> "sam_to_bam" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-65-sam_to_bam>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode12.bam";
  <https://w3id.org/np/snakemake/ruleName> "sam_to_bam" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-66-sam_to_bam>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode13.bam";
  <https://w3id.org/np/snakemake/ruleName> "sam_to_bam" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-67-sam_to_bam>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode15.bam";
  <https://w3id.org/np/snakemake/ruleName> "sam_to_bam" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-68-sam_to_bam>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "alignments/barcode16.bam";
  <https://w3id.org/np/snakemake/ruleName> "sam_to_bam" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-69-sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/barcode10/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-7-alignment_qa_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/barcode10/qualimapReport.html";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-70-sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/barcode11/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-71-sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/barcode12/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-72-sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/barcode13/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-73-sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/barcode15/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-74-sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/barcode16/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-75-standardize_gff>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "references/standardized_genomic.gff";
  <https://w3id.org/np/snakemake/ruleName> "standardize_gff" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-76-total_sample_qa_plot>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "NanoPlot/NanoPlot-report.html";
  <https://w3id.org/np/snakemake/ruleName> "total_sample_qa_plot" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-77-transcriptid_to_gene>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "merged/all_counts_gene.tsv", "merged/transcriptid_to_gene_plot.svg";
  <https://w3id.org/np/snakemake/ruleName> "transcriptid_to_gene" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-8-alignment_qa_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/barcode11/qualimapReport.html";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/job-9-alignment_qa_report>
  a <https://w3id.org/np/snakemake/WorkflowJob>;
  <https://w3id.org/np/snakemake/hasOutput> "qualimap/barcode12/qualimapReport.html";
  <https://w3id.org/np/snakemake/ruleName> "alignment_qa_report" .

<https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/workflow-configuration>
  rdfs:label "from workflow configuration";
  <https://w3id.org/np/snakemake/hasConfigurationFile> <https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE/config-1> .

<https://w3id.org/np/RA1EqFlHdJgd4CTdfRP8XrWDFsVrSHsuXk362eb924i5M/GlobalOSRetreat>
  a <https://w3id.org/fair/3pff/In-Person-Event>, <https://w3id.org/np/RApotRhDip5_Jc5gsSLvEf-wGuYkh5nhcadX_y4ni8Gc4/OSCEvent>;
  dct:date "2026-04-07", "2026-04-11";
  rdfs:label "Open Science Retreat Global - 2026";
  rdfs:seeAlso <https://open.science-retreat.org/OSR26UK/>;
  <https://schema.org/location> "Machynlleth, Wales, UK";
  <https://w3id.org/fair/3pff/has-event-organizer> "https://digital-research.academy/",
    "https://www.wikidata.org/wiki/Q137737148?wprov=acrw1_0";
  <https://w3id.org/fair/connect/has-participating-community> "OpenScience Community members" .

<https://w3id.org/np/RAAA7GCQZOZf8W8EJ51qOZvG-nAT3p0P2ai01fHjBnuTI/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> <https://w3id.org/spaces/Snakemake_Community>;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> <https://w3id.org/spaces/Snakemake_Community>;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RAyGnSBDLneVXhzK8SRwtkU4tN96F_3vSeZVc_SxYMxTk/simple-message-view> .

<https://w3id.org/spaces/Snakemake_Community> a <https://w3id.org/kpxl/gen/terms/Group>,
    <https://w3id.org/kpxl/gen/terms/Space>;
  <https://w3id.org/kpxl/gen/terms/hasObserver> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/hasRole> <https://w3id.org/np/RAqAgIgZHRhzOVArfNvPPGPPfQEUK_b_155d6vGPbMMbc/observer-role>;
  dct:description "The Snakemake Developer Community is a support group for software packages of the Snakemake Workflow Management System. It organizes events such as hackathons and workshops revolving around a better and reproducible data analysis.";
  rdfs:label "Snakemake Community";
  owl:sameAs <https://snakemake.github.io/>;
  <https://w3id.org/kpxl/gen/terms/hasAdmin> orcid:0000-0003-2408-7588 .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/config-1> dct:identifier
    "config/config.yaml";
  <https://schema.org/text> """samples:
  A: data/samples/A.fastq
  B: data/samples/B.fastq

""" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/dataset> a <https://schema.org/Dataset>;
  <https://w3id.org/np/snakemake/describesWorkflow> <https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4>;
  <https://w3id.org/np/snakemake/generatedAt> "2026-03-17T19:26:28.393653+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>;
  <https://w3id.org/np/snakemake/hasWorkflowRun> <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/workflowrun> .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-1>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 1;
  <https://w3id.org/np/snakemake/parameterValue> "-R '@RG\\tID:{sample}\\tSM:{sample}'" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-2>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 2;
  <https://w3id.org/np/snakemake/parameterValue> "samtools" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-3>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 3;
  <https://w3id.org/np/snakemake/parameterValue> "coordinate" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-4>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 4;
  <https://w3id.org/np/snakemake/parameterValue> "" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-samtools_index-1>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 1;
  <https://w3id.org/np/snakemake/parameterValue> "" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-all> a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasInput> "calls/all.vcf", "calls/positions.png", "calls/quals.png";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "all";
  <https://w3id.org/np/snakemake/ruleName> "all" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-bcftools_call>
  a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "calls/all.vcf";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/bcftools.yml", "shell";
  <https://w3id.org/np/snakemake/ruleName> "bcftools_call" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-bwa_mem> a
    <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_reads/A.bam", "sorted_reads/B.bam",
    "sorted_reads/{sample}.bam";
  <https://w3id.org/np/snakemake/hasParameterization> <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-1>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-2>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-3>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-bwa_mem-4>;
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/bwa.yml", "v8.1.1/bio/bwa/mem";
  <https://w3id.org/np/snakemake/parametersJSON> "[\"-R '@RG\\\\tID:{sample}\\\\tSM:{sample}'\", \"samtools\", \"coordinate\", \"\"]";
  <https://w3id.org/np/snakemake/ruleName> "bwa_mem" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-plot_positions>
  a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "calls/positions.png";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/matplotlib.yml", "scripts/plot-positions.py";
  <https://w3id.org/np/snakemake/ruleName> "plot_positions" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-plot_quals>
  a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "calls/quals.png";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/matplotlib.yml", "scripts/plot-quals.py";
  <https://w3id.org/np/snakemake/ruleName> "plot_quals" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-samtools_index>
  a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_reads/A.bam.bai", "sorted_reads/B.bam.bai",
    "sorted_reads/{sample}.bam.bai";
  <https://w3id.org/np/snakemake/hasParameterization> <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/param-samtools_index-1>;
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/samtools.yml", "v5.7.0/bio/samtools/index";
  <https://w3id.org/np/snakemake/parametersJSON> "[\"\"]";
  <https://w3id.org/np/snakemake/ruleName> "samtools_index" .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/workflow-configuration>
  rdfs:label "from workflow configuration";
  <https://w3id.org/np/snakemake/hasConfigurationFile> <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/config-1> .

<https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/workflowrun> a
    <https://w3id.org/np/snakemake/WorkflowRun>;
  <https://w3id.org/np/snakemake/description> "";
  <https://w3id.org/np/snakemake/hasConfigurationSection> <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/workflow-configuration>;
  <https://w3id.org/np/snakemake/hasRule> <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-all>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-bcftools_call>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-bwa_mem>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-plot_positions>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-plot_quals>,
    <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/rule-samtools_index> .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/dataset> a <https://schema.org/Dataset>;
  <https://w3id.org/np/snakemake/describesWorkflow> <https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4>;
  <https://w3id.org/np/snakemake/generatedAt> "2026-03-17T16:56:38.233861+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>;
  <https://w3id.org/np/snakemake/hasSummary> <https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/workflowsummary>;
  <https://w3id.org/np/snakemake/hasWorkflowRun> <https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/workflowrun> .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-1>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 1;
  <https://w3id.org/np/snakemake/parameterValue> "-R '@RG\\tID:{sample}\\tSM:{sample}'" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-2>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 2;
  <https://w3id.org/np/snakemake/parameterValue> "samtools" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-3>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 3;
  <https://w3id.org/np/snakemake/parameterValue> "coordinate" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-4>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 4;
  <https://w3id.org/np/snakemake/parameterValue> "" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-samtools_index-1>
  a <https://w3id.org/np/snakemake/Parameterization>;
  <https://w3id.org/np/snakemake/parameterIndex> 1;
  <https://w3id.org/np/snakemake/parameterValue> "" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/rule-all> a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "all";
  <https://w3id.org/np/snakemake/ruleName> "all" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/rule-bcftools_call>
  a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "calls/all.vcf";
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/bcftools.yml", "shell";
  <https://w3id.org/np/snakemake/ruleName> "bcftools_call" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/rule-bwa_mem> a
    <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "sorted_reads/A.bam", "sorted_reads/B.bam",
    "sorted_reads/{sample}.bam";
  <https://w3id.org/np/snakemake/hasParameterization> <https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-1>,
    <https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-2>,
    <https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-3>,
    <https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/param-bwa_mem-4>;
  <https://w3id.org/np/snakemake/hasSoftwarePackage> "envs/bwa.yml", "v8.1.1/bio/bwa/mem";
  <https://w3id.org/np/snakemake/parametersJSON> "[\"-R '@RG\\\\tID:{sample}\\\\tSM:{sample}'\", \"samtools\", \"coordinate\", \"\"]";
  <https://w3id.org/np/snakemake/ruleName> "bwa_mem" .

<https://w3id.org/np/RAxKHcmY3zCuvwNk8whzmfZjoo_tER30Rxw8QZP2ctr3s/rule-plot_positions>
  a <https://w3id.org/np/snakemake/WorkflowRule>;
  <https://w3id.org/np/snakemake/hasOutput> "calls/positions.png";
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dct:title rdfs:label "has the title", "has title", "has title" .

rdf:type rdfs:label "is a", "is a", "is a" .

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<https://schema.org/datePublished> rdfs:label "was published on" .

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<https://schema.org/result> rdfs:label "results from", "reports performance results" .

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<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/assertion> a nt:AssertionTemplate;
  dct:description "This template can be used to define a Retreat - describe the purpose, here.";
  rdfs:label "Defining a Retreat";
  nt:hasStatement <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st01>,
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st02>, <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st03>,
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st04>, <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st05>,
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st06>, <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st07>,
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st08>, <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st09>,
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st10>, <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st11>,
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st12>;
  nt:hasTag "Events" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/community> a nt:ValuePlaceholder;
  rdfs:label "community - a community that has partecipated in the event" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/date> a nt:LiteralPlaceholder;
  rdfs:label "(starting) date of the event (e.g. 2020-12-31)";
  nt:hasRegex "[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/end-time> a nt:LiteralPlaceholder .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event> a nt:IntroducedResource,
    nt:LocalResource, nt:UriPlaceholder;
  rdfs:label "short name, used as URI suffix" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event-type> a nt:RestrictedChoicePlaceholder;
  nt:possibleValue <https://w3id.org/fair/3pff/Hybrid-Event>, <https://w3id.org/fair/3pff/In-Person-Event>,
    <https://w3id.org/fair/3pff/Virtual-Event> .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/finish-date> a
    nt:LiteralPlaceholder;
  rdfs:label "finish date of the event (e.g. 2020-12-31)" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/location> a nt:LiteralPlaceholder;
  rdfs:label "location of the event (URL or name)" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/name> a nt:LiteralPlaceholder;
  rdfs:label "the name of the event" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/online-resource>
  a nt:UriPlaceholder;
  rdfs:label "online resource" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/organizer> a nt:LiteralPlaceholder;
  rdfs:label "organizer of the event (ROR, URL or name)" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/sponsor> a nt:ValuePlaceholder;
  rdfs:label "sponsor of the event (ROR or name)" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st01> rdf:object
    <https://w3id.org/np/RApotRhDip5_Jc5gsSLvEf-wGuYkh5nhcadX_y4ni8Gc4/OSCEvent>;
  rdf:predicate rdf:type;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "0" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st02> rdf:object
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/name>;
  rdf:predicate rdfs:label;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "1" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st03> rdf:object
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/date>;
  rdf:predicate dct:date;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "2" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st04> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/finish-date>;
  rdf:predicate dct:date;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "3" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st05> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/start-time>;
  rdf:predicate <https://schema.org/startTime>;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "4" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st06> a nt:OptionalStatement,
    nt:RepeatableStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/organizer>;
  rdf:predicate <https://w3id.org/fair/3pff/has-event-organizer>;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "6" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st07> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/sponsor>;
  rdf:predicate <https://w3id.org/fair/3pff/has-event-sponsor>;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "7" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st08> a nt:OptionalStatement,
    nt:RepeatableStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/community>;
  rdf:predicate <https://w3id.org/fair/connect/has-participating-community>;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "8" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st09> rdf:object
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/online-resource>;
  rdf:predicate rdfs:seeAlso;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "9" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st10> rdf:object
    <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event-type>;
  rdf:predicate rdf:type;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "10" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st11> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/location>;
  rdf:predicate <https://schema.org/location>;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "11" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/st12> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/end-time>;
  rdf:predicate <https://schema.org/endTime>;
  rdf:subject <https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/event>;
  nt:statementOrder "5" .

<https://w3id.org/np/RARTR1yqRy8J4OgLuRlWoxOiZz0lQU6Vd_fgZOc5fcFRg/start-time> a nt:LiteralPlaceholder .

<https://doi.org/10.5281/zenodo.18801920> a dcmitype:Dataset;
  dct:license <https://creativecommons.org/licenses/by/4.0/legalcode>;
  dct:title "Testing data set for a Snakemake differential and splicing isoform detection workflow based on ONT RNA-longseq data";
  <http://purl.org/spar/cito/supports> <https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE>;
  <https://schema.org/maintainer> <https://doi.org/10.5281/zenodo.18801920>;
  <https://schema.org/result> <https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE> .

<http://edamontology.org/format_1929> rdfs:label "FASTA", "FASTA" .

<http://edamontology.org/format_1930> rdfs:label "FASTQ", "FASTQ" .

<http://edamontology.org/format_1934> rdfs:label "fitch program", "fitch program" .

<http://edamontology.org/format_1935> rdfs:label "GCG", "GCG" .

<http://edamontology.org/format_1936> rdfs:label "GenBank format", "GenBank format" .

<http://edamontology.org/format_1937> rdfs:label "genpept", "genpept" .

<http://edamontology.org/format_1938> rdfs:label "GFF2-seq", "GFF2-seq" .

<http://edamontology.org/format_1939> rdfs:label "GFF3-seq", "GFF3-seq" .

<http://edamontology.org/format_1940> rdfs:label "giFASTA format", "giFASTA format" .

<http://edamontology.org/format_1950> rdfs:label "pdbatom", "pdbatom" .

dct:creator rdfs:label "created by", "created by" .

dct:format rdfs:label "needs or produces data format", "needs or produces data format" .

prov:wasDerivedFrom rdfs:label "improves upon method", "improves upon method" .

<https://creativecommons.org/licenses/by/4.0/> rdfs:label "CC-BY-4.0", "CC-BY-4.0" .

<https://schema.org/applicationCategory> rdfs:label "serves purpose", "serves purpose" .

<https://schema.org/applicationSubCategory> rdfs:label "applies to domains", "applies to domains" .

<https://schema.org/codeRepository> rdfs:label "has source repository", "has source repository" .

<https://schema.org/keywords> rdfs:label "has keywords", "has keywords" .

<https://schema.org/learningResourceType> rdfs:label "uses computational approach",
    "uses computational approach" .

<https://schema.org/url> rdfs:label "is accessible via", "is accessible via" .

<https://spdx.org/licenses/Apache-2.0.html> rdfs:label "Apache 2.0", "Apache 2.0" .

<https://spdx.org/licenses/BSD-3-Clause.html> rdfs:label "BSD 3 Clause", "BSD 3 Clause" .

<https://spdx.org/licenses/GPL-3.0.html> rdfs:label "GPL 3.0", "GPL 3.0" .

<https://spdx.org/licenses/MIT.html> rdfs:label "MIT", "MIT" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/applicable-domains>
  a nt:GuidedChoicePlaceholder;
  rdfs:label "applicable research domains";
  nt:possibleValuesFromApi "https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/application-category>
  a nt:GuidedChoicePlaceholder;
  rdfs:label "primary computational purpose";
  nt:possibleValuesFromApi "https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/assertion> a nt:AssertionTemplate;
  dct:description "Template for describing a computational workflow implemented for and supported by a Workflow Management System";
  rdfs:label "Computational Workflow";
  nt:hasNanopubLabelPattern "Method: ${title}";
  nt:hasStatement <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st01>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st02>, <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st03>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st04>, <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st05>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st06>, <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st07>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st08>, <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st09>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st10>, <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st11>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st12>, <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st13>,
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st14>;
  nt:hasTag "Computational Workflow" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/base-method> a
    nt:UriPlaceholder;
  rdfs:label "method this improves upon (DOI or URI)" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/computational-approach>
  a nt:GuidedChoicePlaceholder;
  rdfs:label "computational approach used";
  nt:possibleValuesFromApi "https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/computational-workflow>
  a nt:UriPlaceholder;
  rdfs:label "URI of the workflow repository" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/creator> a nt:UriPlaceholder;
  rdfs:label "ORCID of creator";
  nt:hasPrefix "https://orcid.org/";
  nt:hasPrefixLabel "ORCID (just the 16-digit ID)";
  nt:hasRegex "0000-\\d{4}-\\d{4}-\\d{4}" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/description> a
    nt:LongLiteralPlaceholder;
  rdfs:label "description of what the method does";
  nt:hasRegex "[\\s\\S]{10,1000}" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/doi> a nt:UriPlaceholder;
  rdfs:label "DOI URL";
  nt:hasPrefix "https://doi.org/";
  nt:hasPrefixLabel "DOI (starting with '10.')";
  nt:hasRegex "10.(\\d)+/(\\S)+" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/github-repo> a
    nt:UriPlaceholder;
  rdfs:label "GitHub repository URL" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/input-format> a
    nt:RestrictedChoicePlaceholder;
  rdfs:label "expected input data format";
  nt:hasPrefix "input:";
  nt:hasPrefixLabel "Input:";
  nt:possibleValue <http://edamontology.org/format_1929>, <http://edamontology.org/format_1930>,
    <http://edamontology.org/format_1934>, <http://edamontology.org/format_1935>, <http://edamontology.org/format_1936>,
    <http://edamontology.org/format_1937>, <http://edamontology.org/format_1938>, <http://edamontology.org/format_1939>,
    <http://edamontology.org/format_1940>, <http://edamontology.org/format_1950> .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/keywords> a nt:GuidedChoicePlaceholder;
  rdfs:label "research keywords from Wikidata";
  nt:possibleValuesFromApi "https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/license> a nt:RestrictedChoicePlaceholder;
  rdfs:label "software license";
  nt:possibleValue <https://creativecommons.org/licenses/by/4.0/>, <https://spdx.org/licenses/Apache-2.0.html>,
    <https://spdx.org/licenses/BSD-3-Clause.html>, <https://spdx.org/licenses/GPL-3.0.html>,
    <https://spdx.org/licenses/MIT.html> .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st01> rdf:object
    <https://schema.org/SoftwareSourceCode>;
  rdf:predicate rdf:type;
  rdf:subject <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/computational-workflow> .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st02> rdf:object
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/title>;
  rdf:predicate dct:title;
  rdf:subject <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/computational-workflow> .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st03> rdf:object
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/description>;
  rdf:predicate dct:description;
  rdf:subject <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/computational-workflow> .

<https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/st04> rdf:object
    <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/doi>;
  rdf:predicate <https://schema.org/url>;
  rdf:subject <https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk/computational-workflow> .

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    nt:RepeatableStatement;
  rdf:object <https://w3id.org/np/RAPGpEZJ4__5FKspY1G_xs3cAa6aTGfZFLk81dD_YOEN8/applicable-domains>;
  rdf:predicate <https://schema.org/applicationSubCategory>;
  rdf:subject <https://w3id.org/np/RAPGpEZJ4__5FKspY1G_xs3cAa6aTGfZFLk81dD_YOEN8/computational-workflow> .

<https://w3id.org/np/RAPGpEZJ4__5FKspY1G_xs3cAa6aTGfZFLk81dD_YOEN8/title> a nt:LiteralPlaceholder;
  rdfs:label "title of the Workflow";
  nt:hasRegex "[\\s\\S]{5,200}" .

<https://w3id.org/np/RAPGpEZJ4__5FKspY1G_xs3cAa6aTGfZFLk81dD_YOEN8/workflow-management-system>
  a nt:RestrictedChoicePlaceholder;
  rdfs:label "Workflow Management System", "uses workflow management system";
  nt:possibleValue <https://www.wikidata.org/wiki/Q106286298>, <https://www.wikidata.org/wiki/Q2808660>,
    <https://www.wikidata.org/wiki/Q51293717>, <https://www.wikidata.org/wiki/Q5518091>,
    <https://www.wikidata.org/wiki/Q56291707> .

<https://w3id.org/np/RA_V8BgodumTTzLUEsl-QA1xQBPvgGMYpHmc188tpNLvk/assertion> rdfs:label
    """I think we need to have an \"onboarding SOP\" for
- people who start authenticating others for the first time.
- for 3rd party lecturers who introduce nanopubs in workshops

It could be a slide set or a static part of the homepage or ... anything else without too much effort.

What do you think?""";
  <https://schema.org/about> <https://w3id.org/spaces/nanopub/nanosessions/session28> .

<https://indico.cern.ch/event/1574891/> a <https://w3id.org/fair/3pff/In-Person-Event>,
    <https://w3id.org/np/RApotRhDip5_Jc5gsSLvEf-wGuYkh5nhcadX_y4ni8Gc4/OSCEvent>;
  dct:date "2026-03-09", "2026-03-13";
  rdfs:label "Snakemake Hackathon";
  rdfs:seeAlso <https://indico.cern.ch/event/1574891/>;
  <https://schema.org/location> "Munich, Germany";
  <https://w3id.org/fair/3pff/has-event-organizer> "Christian Meesters", "Clemens Lange",
    "David Lähnemann", "Johannes Köster", "Lukas Heinrich", "Matthew Feickert";
  <https://w3id.org/fair/3pff/has-event-sponsor> <https://w3id.org/np/RAfMWhiOBw0sz1ANQyENyJGRAruP-V53zwk48zh2VcRpY/BASF>;
  <https://w3id.org/fair/connect/has-participating-community> <https://w3id.org/np/RAfMWhiOBw0sz1ANQyENyJGRAruP-V53zwk48zh2VcRpY/Snakemake> .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/assertion> a nt:AssertionTemplate;
  dct:description "This template can be used to define a Hackathon Event.";
  rdfs:label "Defining a Hackathon Event";
  nt:hasStatement <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st01>,
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st02>, <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st03>,
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st04>, <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st05>,
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st06>, <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st07>,
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st08>, <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st09>,
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st10>, <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st11>,
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st12>;
  nt:hasTag "Events" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/community> a nt:ValuePlaceholder;
  rdfs:label "community - a community that has partecipated in the event" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/date> a nt:LiteralPlaceholder;
  rdfs:label "(starting) date of the event (e.g. 2020-12-31)";
  nt:hasRegex "[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/end-time> a nt:LiteralPlaceholder .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event> a nt:IntroducedResource,
    nt:LocalResource, nt:UriPlaceholder;
  rdfs:label "short name, used as URI suffix" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event-type> a nt:RestrictedChoicePlaceholder;
  nt:possibleValue <https://w3id.org/fair/3pff/Hybrid-Event>, <https://w3id.org/fair/3pff/In-Person-Event>,
    <https://w3id.org/fair/3pff/Virtual-Event> .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/finish-date> a
    nt:LiteralPlaceholder;
  rdfs:label "finish date of the event (e.g. 2020-12-31)" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/location> a nt:LiteralPlaceholder;
  rdfs:label "location of the event (URL or name)" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/name> a nt:LiteralPlaceholder;
  rdfs:label "the name of the event" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/online-resource>
  a nt:UriPlaceholder;
  rdfs:label "online resource" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/organizer> a nt:LiteralPlaceholder;
  rdfs:label "organizer of the event (ROR, URL or name)" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/sponsor> a nt:ValuePlaceholder;
  rdfs:label "sponsor of the event (ROR or name)" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st01> rdf:object
    <https://w3id.org/np/RApotRhDip5_Jc5gsSLvEf-wGuYkh5nhcadX_y4ni8Gc4/OSCEvent>;
  rdf:predicate rdf:type;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "0" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st02> rdf:object
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/name>;
  rdf:predicate rdfs:label;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "1" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st03> rdf:object
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/date>;
  rdf:predicate dct:date;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "2" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st04> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/finish-date>;
  rdf:predicate dct:date;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "3" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st05> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/start-time>;
  rdf:predicate <https://schema.org/startTime>;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "4" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st06> a nt:OptionalStatement,
    nt:RepeatableStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/organizer>;
  rdf:predicate <https://w3id.org/fair/3pff/has-event-organizer>;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "6" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st07> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/sponsor>;
  rdf:predicate <https://w3id.org/fair/3pff/has-event-sponsor>;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "7" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st08> a nt:OptionalStatement,
    nt:RepeatableStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/community>;
  rdf:predicate <https://w3id.org/fair/connect/has-participating-community>;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "8" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st09> rdf:object
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/online-resource>;
  rdf:predicate rdfs:seeAlso;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "9" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st10> rdf:object
    <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event-type>;
  rdf:predicate rdf:type;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "10" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st11> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/location>;
  rdf:predicate <https://schema.org/location>;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "11" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/st12> a nt:OptionalStatement;
  rdf:object <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/end-time>;
  rdf:predicate <https://schema.org/endTime>;
  rdf:subject <https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/event>;
  nt:statementOrder "5" .

<https://w3id.org/np/RA_GErDKQT4g0I980hQ0Di1fNHFL3SwvV-IEjJOSEFsGs/start-time> a nt:LiteralPlaceholder .

<https://w3id.org/np/RAGWCQle2Nn9pJpM0EouVuuvVAnjhmJi8GvUWihqK7I1g/display> a <https://w3id.org/kpxl/gen/terms/ActivatedViewDisplay>,
    <https://w3id.org/kpxl/gen/terms/ViewDisplay>;
  <https://w3id.org/kpxl/gen/terms/appliesTo> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayFor> orcid:0000-0003-2408-7588;
  <https://w3id.org/kpxl/gen/terms/isDisplayOfView> <https://w3id.org/np/RAPngSscVdQ4UeD5-98ZMFEhubZ6eQRs6EsmPbUBFD5L8/planned-event-attendance-view> .

<https://w3id.org/np/RAPrtIpGfmGx3z2r3YziIN6XgHEZ7ZEYz0iZ1dlv3wjPM/assertion> rdfs:label
    """Ah, I was thinking, should the \"Plan to attend\" nanopub template not have a description? A text label, as not all URLs are descriptive?

And there it is! The template is updated. Already!

How about adding the option to link it with another nanopub? A declared event? And the declared event should have a descriptive field, too. ;-)

What do you think?""";
  rdfs:seeAlso <https://w3id.org/np/RAMLjCU1mjqtNw8n_bBxiE2Xk0H_80UlSKMnexH2bqyeQ>;
  <https://schema.org/about> <https://w3id.org/spaces/fenac> .

<https://w3id.org/np/RAQkRgam5soAC8p2audYEK88QTJjhxLqrDWP6siwwkr5c/deRSE26> a <http://example.org/Event>,
    owl:NamedIndividual;
  dct:description """The German Research Software Engineering (deRSE26) takes place from March 3 to March 5, 2026 at the University of Stuttgart.

Contributions from all computational fields are welcome.""";
  rdfs:label "German Research Software Engineering Conference 2026";
  rdfs:seeAlso <https://events.hifis.net/event/2945/overview> .

<https://w3id.org/np/RAoYy0bW33mUXlf6MOe3Q09AMualJr4D99z9vtEHFVsgE/Continuous_Integration_101>
  a <https://w3id.org/fair/connect/FAIR-Training-Material>;
  dct:MediaType <https://w3id.org/np/RAoYy0bW33mUXlf6MOe3Q09AMualJr4D99z9vtEHFVsgE/TeX/PDF>;
  dct:created "9. October 2025";
  dct:creator orcid:0000-0003-2408-7588;
  schema:url <https://github.com/cmeesters/CI_course>;
  rdfs:comment "An introduction to Continuous Integration";
  rdfs:label "Continuous Integration Course";
  skos:related <http://edamontology.org/topic_3307>, <http://edamontology.org/topic_3316>,
    <http://purl.obolibrary.org/obo/NCIT_C18470> .

<https://doi.org/10.14279/eceasst.v83.2600> a <http://purl.org/spar/fabio/ScholarlyWork>;
  <http://purl.org/spar/cito/cites> <http://dx.doi.org/10.1007/978-3-031-02309-5_2>,
    <http://dx.doi.org/10.1016/j.tibtech.2012.02.002>, <http://dx.doi.org/10.1038/nbt.3820>,
    <http://dx.doi.org/10.1038/s41562-016-0021>, <http://dx.doi.org/10.1038/s41592-018-0046-7>,
    <http://dx.doi.org/10.1109/MCSE.2020.2996073>, <http://dx.doi.org/10.1145/3159450.3159530>,
    <http://dx.doi.org/10.12688/f1000research.121714.2>, <http://dx.doi.org/10.12688/f1000research.29032.2>,
    <http://dx.doi.org/10.3390/molecules28030988>, <http://dx.doi.org/10.3390/ph15091046>,
    <http://dx.doi.org/10.3390/ph17010080>, <http://dx.doi.org/10.4103/EHP.EHP_25_22>,
    <http://dx.doi.org/10.5281/ZENODO.1310023>, <https://jinja.palletsprojects.com/>,
    <https://modules.sourceforge.net/>;
  <http://purl.org/spar/cito/citesAsAuthority> <http://dx.doi.org/10.1186/1472-6920-11-37>;
  <http://purl.org/spar/cito/citesAsDataSource> <http://dx.doi.org/10.1145/2818314.2818335>;
  <http://purl.org/spar/cito/citesAsEvidence> <http://dx.doi.org/10.1016/j.chb.2013.04.001>,
    <http://dx.doi.org/10.1016/j.heliyon.2018.e01057>, <http://dx.doi.org/10.1080/08993408.2019.1565235>,
    <http://dx.doi.org/10.1080/10494820.2020.1817761>, <http://dx.doi.org/10.1145/1044550.1041673>,
    <http://dx.doi.org/10.1145/1595496.1562930>, <http://dx.doi.org/10.1145/2543882.2543884>,
    <http://dx.doi.org/10.1145/2724660.2724681>, <http://dx.doi.org/10.1145/3279720.3279725>,
    <http://dx.doi.org/10.1177/1745691616635600>, <http://dx.doi.org/10.1177/1745691616652873>,
    <http://dx.doi.org/10.1186/2047-217X-2-9>, <http://dx.doi.org/10.1186/s12859-020-03565-8>,
    <http://dx.doi.org/10.1371/journal.pcbi.1007531>, <http://dx.doi.org/10.3102/0034654317751919>,
    <http://dx.doi.org/10.4103/EHP.EHP_25_22>, <https://dl.acm.org/doi/10.5555/1151869.1151890>;
  <http://purl.org/spar/cito/citesAsPotentialSolution> <http://dx.doi.org/10.1002/spe.3075> .

<https://w3id.org/np/RAkl3FHfd8WOxmYxvROTK-UIUnW0n80ATIO5sRONctfYM#Snakemake_HPC_Teaching_Material>
  a <https://w3id.org/fair/connect/FAIR-Training-Material>;
  dct:MediaType <https://w3id.org/np/RAkl3FHfd8WOxmYxvROTK-UIUnW0n80ATIO5sRONctfYM#PDF>;
  dct:creator orcid:0000-0001-7601-9873;
  schema:url <https://github.com/snakemake/snakemake-hpc-teaching-material>;
  rdfs:comment "Data Analysis Workflow on HPC Systems";
  rdfs:label "Snakemake HPC Teaching Material";
  rdfs:seeAlso <https://eceasst.org/index.php/eceasst/article/view/2600>;
  skos:related <http://aims.fao.org/aos/agrovoc/c_4318>, <http://edamontology.org/topic_3307>,
    <http://edamontology.org/topic_3316>, <http://edamontology.org/topic_3318> .

<https://doi.org/10.3390/molecules28030988> a <http://purl.org/spar/fabio/ScholarlyWork>;
  <http://purl.org/spar/cito/cites> <https://doi.org/10.1016/S2666-5247(21)00278-0>,
    <https://doi.org/10.1016/j.talanta.2014.09.038>, <https://doi.org/10.1021/acs.jnatprod.9b01285>,
    <https://doi.org/10.1089/adt.2011.0380>, <https://doi.org/10.1186/1758-2946-3-33>,
    <https://doi.org/10.1371/annotation/a0dde376-2eb1-4ce3-8887-d29f5ba6f162>, <https://doi.org/10.18632/oncotarget.7605>;
  <http://purl.org/spar/cito/citesAsAuthority> <https://doi.org/10.1007/s40265-020-01378-w>,
    <https://doi.org/10.1016%2FS0065-3527(08)60286-9>, <https://doi.org/10.1074/jbc.M110.120014>,
    <https://doi.org/10.23750/abm.v91i1.9397>;
  <http://purl.org/spar/cito/citesAsDataSource> <https://doi.org/10.1038/s41467-020-17495-9>,
    <https://doi.org/10.1073/pnas.2100170118>, <https://doi.org/10.1371/journal.ppat.1002059>;
  <http://purl.org/spar/cito/citesAsEvidence> <https://doi.org/10.1001/jama.2020.2648>,
    <https://doi.org/10.1002/jmv.25678>, <https://doi.org/10.1016/bs.aivir.2016.08.008>,
    <https://doi.org/10.1016/j.chom.2020.02.001>, <https://doi.org/10.1016/j.ijsu.2020.04.018>,
    <https://doi.org/10.1038/nature09489>, <https://doi.org/10.1038/s41467-020-17495-9>,
    <https://doi.org/10.1039/D1RA01989A>, <https://doi.org/10.1128/JVI.00407-08>, <https://doi.org/10.1146/annurev-virology-100114-055218>,
    <https://doi.org/10.1155/2013/963248>, <https://doi.org/10.1371/journal.ppat.1002059>,
    <https://doi.org/10.7150/ijbs.45472>;
  <http://purl.org/spar/cito/citesAsPotentialSolution> <https://doi.org/10.1126/scisignal.abe1202>;
  <http://purl.org/spar/cito/citesAsRecommendedReading> <https://doi.org/10.1186/s13321-020-00424-9>,
    <https://doi.org/10.3390/v13040538>;
  <http://purl.org/spar/cito/citesAsRelated> <https://doi.org/10.1002/slct.202103658>;
  <http://purl.org/spar/cito/citesForInformation> <https://doi.org/10.1080/07853890.2022.2034936> .

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