@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix ns1: <https://w3id.org/np/snakemake/> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <https://schema.org/> .
@prefix sub: <https://w3id.org/np/RAPaopgiLByaOJf5SMIEVQEYRcfdkeLr0pjYn9J2dk8ak/> .
@prefix this: <https://w3id.org/np/RAPaopgiLByaOJf5SMIEVQEYRcfdkeLr0pjYn9J2dk8ak> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

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

sub:assertion {
  sub:config-1 dcterms:identifier "config.yaml";
    schema:text """samples:
  A: data/samples/A.fastq
  B: data/samples/B.fastq

bwa_map:
  rg: \"@RG\\\\tID:{sample}\\\\tSM:{sample}\"""" .
  
  sub:config-2 dcterms:identifier "config.yaml";
    schema:text """samples:
  A: data/samples/A.fastq
  B: data/samples/B.fastq

bwa_map:
  rg: \"@RG\\\\tID:{sample}\\\\tSM:{sample}\"""" .
  
  sub:dataset a schema:Dataset;
    ns1:describesWorkflow "RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4";
    ns1:generatedAt "2026-06-09T14:21:05.407308+00:00"^^xsd:dateTime;
    ns1:hasConfigurationSection sub:workflow-configuration;
    ns1:hasRuleSection sub:workflow-rules .
  
  sub:job-1-bcftools_call a ns1:WorkflowJob;
    ns1:hasOutput "calls/all.vcf";
    ns1:ruleName "bcftools_call" .
  
  sub:job-2-bwa_mem a ns1:WorkflowJob;
    ns1:hasOutput "sorted_reads/A.bam";
    ns1:ruleName "bwa_mem" .
  
  sub:job-3-bwa_mem a ns1:WorkflowJob;
    ns1:hasOutput "sorted_reads/B.bam";
    ns1:ruleName "bwa_mem" .
  
  sub:job-4-plot_positions a ns1:WorkflowJob;
    ns1:hasOutput "calls/positions.png";
    ns1:ruleName "plot_positions" .
  
  sub:job-5-plot_quals a ns1:WorkflowJob;
    ns1:hasOutput "calls/quals.svg";
    ns1:ruleName "plot_quals" .
  
  sub:job-6-samtools_index a ns1:WorkflowJob;
    ns1:hasOutput "sorted_reads/A.bam.bai";
    ns1:ruleName "samtools_index" .
  
  sub:job-7-samtools_index a ns1:WorkflowJob;
    ns1:hasOutput "sorted_reads/B.bam.bai";
    ns1:ruleName "samtools_index" .
  
  sub:rule-bcftools_call ns1:hasInput "data/genome.fa", "sorted_reads/A.bam", "sorted_reads/A.bam.bai",
      "sorted_reads/B.bam", "sorted_reads/B.bam.bai";
    ns1:hasOutput "calls/all.vcf" .
  
  sub:rule-bwa_mem ns1:hasInput "data/genome.fa.amb", "data/genome.fa.ann", "data/genome.fa.pac",
      "data/genome.fa.sa";
    ns1:hasOutput "sorted_reads/{sample}.bam";
    ns1:hasSoftwarePackage "github.com/snakemake/snakemake-wrappers/bio/bwa/mem/environment.yaml@v5.7.0" .
  
  sub:rule-plot_positions ns1:hasInput "calls/all.vcf";
    ns1:hasOutput "calls/positions.png" .
  
  sub:rule-plot_quals ns1:hasInput "calls/all.vcf";
    ns1:hasOutput "calls/quals.svg" .
  
  sub:rule-samtools_index ns1:hasInput "sorted_reads/{sample}.bam";
    ns1:hasOutput "sorted_reads/{sample}.bam.bai";
    ns1:hasSoftwarePackage "github.com/snakemake/snakemake-wrappers/bio/samtools/index/environment.yaml@v5.7.0" .
  
  sub:workflow-configuration rdfs:label "from workflow configuration";
    ns1:hasConfigurationFile sub:config-1, sub:config-2 .
  
  sub:workflow-rules rdfs:label "workflow rules";
    ns1:hasWorkflowRule sub:rule-bcftools_call, sub:rule-bwa_mem, sub:rule-plot_positions,
      sub:rule-plot_quals, sub:rule-samtools_index .
}

sub:provenance {
  sub:assertion prov:generatedAtTime "2026-06-09T16:21:05.451297+02:00"^^xsd:dateTime;
    prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}

sub:pubinfo {
  this: dcterms:created "2026-06-09T14:21:05.407308+00:00"^^xsd:dateTime;
    dcterms:creator orcid:0000-0003-2408-7588;
    npx:hasNanopubType schema:Dataset;
    npx:signedBy orcid:0000-0003-2408-7588;
    rdfs:label "Snakemake workflow metadata: RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4";
    prov:generatedAtTime "2026-06-09T16:21:05.451297+02:00"^^xsd:dateTime;
    prov:wasAttributedTo orcid:0000-0003-2408-7588 .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB";
    npx:hasSignature "YJi+0JKjA28Qn6TAyXo5peTdT08c/mRJpIYFz4t5qV+VvsZQd1PObuT6iRk0qCWEiFuekLvueibkRkBTags+eJOFHTiaY5hbsUgByOQex0w33uQsDhngH+2W3Y5OjeqPh76ekTuUL4KvHflDY52HZHUGE2zzBC3YgTBVh9Lkl4plAdMWIy9H6znkd3H7tAytady8Qh4EEcxFyXFdqTE9W3+2/FnpzYm2uobsIq7ndt3lK6dJhkmWtzlPmGF5tqJAOJ1B4pU6QAjE7MsZBFgiuvN1IhYuDWABEdXlbhRYvgpt6z7Gs9AMYFuqYNea2gmrNCshj9WpdbLeNHLS6VsGFA==";
    npx:hasSignatureTarget this:;
    npx:signedBy orcid:0000-0003-2408-7588 .
}