@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/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg/> .
@prefix this: <https://w3id.org/np/RAz9ihRB2SrMYmy_tjuAPvff_suzlYkckGoRdStH8KKbg> .
@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/config.yaml";
    schema:text """samples:
  A: data/samples/A.fastq
  B: data/samples/B.fastq

""" .
  
  sub:dataset a schema:Dataset;
    ns1:describesWorkflow <https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4>;
    ns1:generatedAt "2026-03-17T19:26:28.393653+00:00"^^xsd:dateTime;
    ns1:hasWorkflowRun sub:workflowrun .
  
  sub:param-bwa_mem-1 a ns1:Parameterization;
    ns1:parameterIndex "1"^^xsd:integer;
    ns1:parameterValue "-R '@RG\\tID:{sample}\\tSM:{sample}'" .
  
  sub:param-bwa_mem-2 a ns1:Parameterization;
    ns1:parameterIndex "2"^^xsd:integer;
    ns1:parameterValue "samtools" .
  
  sub:param-bwa_mem-3 a ns1:Parameterization;
    ns1:parameterIndex "3"^^xsd:integer;
    ns1:parameterValue "coordinate" .
  
  sub:param-bwa_mem-4 a ns1:Parameterization;
    ns1:parameterIndex "4"^^xsd:integer;
    ns1:parameterValue "" .
  
  sub:param-samtools_index-1 a ns1:Parameterization;
    ns1:parameterIndex "1"^^xsd:integer;
    ns1:parameterValue "" .
  
  sub:rule-all a ns1:WorkflowRule;
    ns1:hasInput "calls/all.vcf", "calls/positions.png", "calls/quals.png";
    ns1:hasSoftwarePackage "all";
    ns1:ruleName "all" .
  
  sub:rule-bcftools_call a ns1:WorkflowRule;
    ns1:hasOutput "calls/all.vcf";
    ns1:hasSoftwarePackage "envs/bcftools.yml", "shell";
    ns1:ruleName "bcftools_call" .
  
  sub:rule-bwa_mem a ns1:WorkflowRule;
    ns1:hasOutput "sorted_reads/A.bam", "sorted_reads/B.bam", "sorted_reads/{sample}.bam";
    ns1:hasParameterization sub:param-bwa_mem-1, sub:param-bwa_mem-2, sub:param-bwa_mem-3,
      sub:param-bwa_mem-4;
    ns1:hasSoftwarePackage "envs/bwa.yml", "v8.1.1/bio/bwa/mem";
    ns1:parametersJSON "[\"-R '@RG\\\\tID:{sample}\\\\tSM:{sample}'\", \"samtools\", \"coordinate\", \"\"]";
    ns1:ruleName "bwa_mem" .
  
  sub:rule-plot_positions a ns1:WorkflowRule;
    ns1:hasOutput "calls/positions.png";
    ns1:hasSoftwarePackage "envs/matplotlib.yml", "scripts/plot-positions.py";
    ns1:ruleName "plot_positions" .
  
  sub:rule-plot_quals a ns1:WorkflowRule;
    ns1:hasOutput "calls/quals.png";
    ns1:hasSoftwarePackage "envs/matplotlib.yml", "scripts/plot-quals.py";
    ns1:ruleName "plot_quals" .
  
  sub:rule-samtools_index a ns1:WorkflowRule;
    ns1:hasOutput "sorted_reads/A.bam.bai", "sorted_reads/B.bam.bai", "sorted_reads/{sample}.bam.bai";
    ns1:hasParameterization sub:param-samtools_index-1;
    ns1:hasSoftwarePackage "envs/samtools.yml", "v5.7.0/bio/samtools/index";
    ns1:parametersJSON "[\"\"]";
    ns1:ruleName "samtools_index" .
  
  sub:workflow-configuration rdfs:label "from workflow configuration";
    ns1:hasConfigurationFile sub:config-1 .
  
  sub:workflowrun a ns1:WorkflowRun;
    ns1:description "";
    ns1:hasConfigurationSection sub:workflow-configuration;
    ns1:hasRule sub:rule-all, 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 "2026-03-17T20:26:28.425702"^^xsd:dateTime;
    prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}

sub:pubinfo {
  this: dcterms:created "2026-03-17T19:26:28.393653+00:00"^^xsd:dateTime;
    dcterms:creator orcid:0000-0003-2408-7588;
    npx:hasNanopubType schema:Dataset;
    rdfs:label "Snakemake workflow metadata: https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4";
    prov:generatedAtTime "2026-03-17T20:26:28.425702"^^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 "CH5+xPEIySSnPKlNQRMR9lP1Se/eXTtiKMcPYx1gtzD8iXwM1mS7a1JxlBFvyzYoqTTXomqaqElWuDrHcGlBmuDqtusQfZIU7Yd0xfZRGdC7ErTjfmVnxEfyY3eAj2VeLNLjvD0xDknxC9UaEG6EVSiHcxBr9TYC+qd9YShSFq9/+A8LjGfUmGVyymw79h+qkcNGRMEqhdQ8h6OoZA/f6T8MCVRGMv2bwK6qaQCTHJTbRaNuzYNXVhfwzbZJscf/esPH+b8Df1kQuqeImE1kSrsRcSztCs0uCZvd7VGVwBP3e+/VALepCeXV+9dkBZwj8BZw0Vx8nc+LUDWlC2arJA==";
    npx:hasSignatureTarget this:;
    npx:signedBy orcid:0000-0003-2408-7588 .
}