Nanopublications

@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: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}

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 ;
    ns1:parameterValue "-R '@RG\\tID:{sample}\\tSM:{sample}'" .
  sub:param-bwa_mem-2 a ns1:Parameterization ;
    ns1:parameterIndex 2 ;
    ns1:parameterValue "samtools" .
  sub:param-bwa_mem-3 a ns1:Parameterization ;
    ns1:parameterIndex 3 ;
    ns1:parameterValue "coordinate" .
  sub:param-bwa_mem-4 a ns1:Parameterization ;
    ns1:parameterIndex 4 ;
    ns1:parameterValue "" .
  sub:param-samtools_index-1 a ns1:Parameterization ;
    ns1:parameterIndex 1 ;
    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 .
}