https://w3id.org/np/RAJkSUwwg_u_dDgCpvO6QjfwAeyj_GfMiLVGCjZxfEA2k
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@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 schema: <https://schema.org/> .
@prefix sub: <https://w3id.org/np/RAJkSUwwg_u_dDgCpvO6QjfwAeyj_GfMiLVGCjZxfEA2k/> .
@prefix this: <https://w3id.org/np/RAJkSUwwg_u_dDgCpvO6QjfwAeyj_GfMiLVGCjZxfEA2k> .
@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 {
<http://purl.org/nanopub/temp/np-3ed6d70b-7d4a-4c02-9ef4-ddfceb668e77> a schema:Dataset;
ns1:describesWorkflow <https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4>;
ns1:generatedAt "2026-03-12T23:46:19.400914+00:00"^^xsd:dateTime;
ns1:hasSummary <http://purl.org/nanopub/temp/ws-19dbbdbd-4f4d-4f12-bd93-a594d5c75e3c>;
ns1:hasWorkflowRun <http://purl.org/nanopub/temp/wr-12ebd539-8a35-4149-83e1-822249e0afff> .
<http://purl.org/nanopub/temp/param-bwa_mem-1> a ns1:Parameterization;
ns1:parameterIndex "1"^^xsd:integer;
ns1:parameterValue "-R '@RG\\tID:{sample}\\tSM:{sample}'" .
<http://purl.org/nanopub/temp/param-bwa_mem-2> a ns1:Parameterization;
ns1:parameterIndex "2"^^xsd:integer;
ns1:parameterValue "samtools" .
<http://purl.org/nanopub/temp/param-bwa_mem-3> a ns1:Parameterization;
ns1:parameterIndex "3"^^xsd:integer;
ns1:parameterValue "coordinate" .
<http://purl.org/nanopub/temp/param-bwa_mem-4> a ns1:Parameterization;
ns1:parameterIndex "4"^^xsd:integer;
ns1:parameterValue "" .
<http://purl.org/nanopub/temp/param-samtools_index-1> a ns1:Parameterization;
ns1:parameterIndex "1"^^xsd:integer;
ns1:parameterValue "" .
<http://purl.org/nanopub/temp/rule-all> a ns1:WorkflowRule;
ns1:hasSoftwarePackage "all";
ns1:ruleName "all" .
<http://purl.org/nanopub/temp/rule-bcftools_call> a ns1:WorkflowRule;
ns1:hasOutput "calls/all.vcf";
ns1:hasSoftwarePackage "envs/bcftools.yml", "shell";
ns1:ruleName "bcftools_call" .
<http://purl.org/nanopub/temp/rule-bwa_mem> a ns1:WorkflowRule;
ns1:hasOutput "sorted_reads/A.bam", "sorted_reads/B.bam", "sorted_reads/{sample}.bam";
ns1:hasParameterization <http://purl.org/nanopub/temp/param-bwa_mem-1>, <http://purl.org/nanopub/temp/param-bwa_mem-2>,
<http://purl.org/nanopub/temp/param-bwa_mem-3>, <http://purl.org/nanopub/temp/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" .
<http://purl.org/nanopub/temp/rule-plot_positions> a ns1:WorkflowRule;
ns1:hasOutput "calls/positions.png";
ns1:hasSoftwarePackage "envs/matplotlib.yml", "scripts/plot-positions.py";
ns1:ruleName "plot_positions" .
<http://purl.org/nanopub/temp/rule-plot_quals> a ns1:WorkflowRule;
ns1:hasOutput "calls/quals.png";
ns1:hasSoftwarePackage "envs/matplotlib.yml", "scripts/plot-quals.py";
ns1:ruleName "plot_quals" .
<http://purl.org/nanopub/temp/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 <http://purl.org/nanopub/temp/param-samtools_index-1>;
ns1:hasSoftwarePackage "envs/samtools.yml", "v5.7.0/bio/samtools/index";
ns1:parametersJSON "[\"\"]";
ns1:ruleName "samtools_index" .
<http://purl.org/nanopub/temp/wr-12ebd539-8a35-4149-83e1-822249e0afff> a ns1:WorkflowRun;
ns1:configJSON "{\"samples\": {\"A\": \"data/samples/A.fastq\", \"B\": \"data/samples/B.fastq\"}}";
ns1:configfile "config/config.yaml";
ns1:dagSource "Snakefile", "config/config.yaml", "envs/bcftools.yml", "envs/bwa.yml",
"envs/matplotlib.yml", "envs/samtools.yml", "scripts/plot-positions.py", "scripts/plot-quals.py";
ns1:description "";
ns1:hasRule <http://purl.org/nanopub/temp/rule-all>, <http://purl.org/nanopub/temp/rule-bcftools_call>,
<http://purl.org/nanopub/temp/rule-bwa_mem>, <http://purl.org/nanopub/temp/rule-plot_positions>,
<http://purl.org/nanopub/temp/rule-plot_quals>, <http://purl.org/nanopub/temp/rule-samtools_index>;
ns1:includedSnakefile "/home/meesters/Documents/Teaching/snakemake-hpc-teaching-material/snakemake-tutorial/Snakefile";
ns1:mainSnakefile "/home/meesters/Documents/Teaching/snakemake-hpc-teaching-material/snakemake-tutorial/Snakefile";
ns1:workflowMetadataJSON "{}" .
<http://purl.org/nanopub/temp/ws-19dbbdbd-4f4d-4f12-bd93-a594d5c75e3c> a ns1:WorkflowSummary;
ns1:numberOfJobs "8"^^xsd:integer;
ns1:numberOfResults "2"^^xsd:integer;
ns1:numberOfRules "6"^^xsd:integer .
}
sub:provenance {
sub:assertion prov:generatedAtTime "2026-03-13T00:46:19.435998"^^xsd:dateTime;
prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}
sub:pubinfo {
this: prov:generatedAtTime "2026-03-13T00:46:19.435998"^^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 "CsZhIYGA8HMokB9nNL9ZE26JirWl7b2Tj9LgWxe0yx9x/EGEKAySXjshsq2AbMY9FrF9MGCzqIxMwWkYiJmGgDW2T/hrocVJS9MXbmFwiskFt98puFC2n/pGnmA+exJknw2vqlsPemDOU2KIzkLapWA2ZqEFWNmH9noraiF+1j6CusQXo4sU8v6CYrLGS+xjUYC0kCutuvpcJnAAj2Z1Lsi1NQ++PwESTsvuF+epB0VebUJDiPY/byCNciaTq8rwaiVxvifY+8wAB3ui4SJowpvUq0MgT4vsTl8/TycqSi1fC2BE3jgOgFZhqmResXX0jT1z2yUtvSCEswyoRaozQA==";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0000-0003-2408-7588 .
}