https://w3id.org/np/RA0Py76if_ufiwsR10hOQh2AwHhupRkqUzg8o2AfPHF3Y
.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/RA0Py76if_ufiwsR10hOQh2AwHhupRkqUzg8o2AfPHF3Y/> .
@prefix this: <https://w3id.org/np/RA0Py76if_ufiwsR10hOQh2AwHhupRkqUzg8o2AfPHF3Y> .
@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-889e9c94-2e0e-4f50-a402-dac482c9d14e> a schema:Dataset;
ns1:describesWorkflow <https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4>;
ns1:generatedAt "2026-03-13T14:56:00.669700+00:00"^^xsd:dateTime;
ns1:hasSummary <http://purl.org/nanopub/temp/ws-c46fa39d-d42f-46db-8fc6-75465b9e741b>;
ns1:hasWorkflowRun <http://purl.org/nanopub/temp/wr-e0de72f5-baad-4a8a-bc68-e38b12a47dd8> .
<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-e0de72f5-baad-4a8a-bc68-e38b12a47dd8> 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-c46fa39d-d42f-46db-8fc6-75465b9e741b> a ns1:WorkflowSummary;
ns1:numberOfJobs "8"^^xsd:integer;
ns1:numberOfResults "2"^^xsd:integer;
ns1:numberOfRules "6"^^xsd:integer .
}
sub:provenance {
sub:assertion prov:generatedAtTime "2026-03-13T15:56:00.698781"^^xsd:dateTime;
prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}
sub:pubinfo {
this: prov:generatedAtTime "2026-03-13T15:56:00.698781"^^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 "XLpj3h5lBHdnR7H5dBpBYMFlqD6e4MC4e1sfDW4JjeO7uOq3xR4JIvhM9M5yFoLJrxEdoczvEdeUYKZg2TtLGLr1DoPXnF6W+mXIL8QkX0XrxykP1ZHAag33IqtqqDXDnul1oWgxBOShmVo+Cze9TVrBb50dvPKYg6Yc/WjXAxqTyJBlPvzN5KOYv49PaEblNp+xCX7S+ALkIaPkiy+atp+a1oUgcT5z9hizwEiTto/24WG7qW90mGxS3nNj3wSr7DC8GCMQ1mO/cP+VRO1bk1OqThtyTwTjYnj0QnjTTwkjgoDlFgNUpwkVXTCpi8NqfcN8L9eGQy2drGjgh1N4qQ==";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0000-0003-2408-7588 .
}