[
    {
        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/provenance",
        "@graph": [
            {
                "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/assertion",
                "http://www.w3.org/ns/prov#generatedAtTime": [
                    {
                        "@value": "2026-03-13T15:28:27.526317",
                        "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
                    }
                ],
                "http://www.w3.org/ns/prov#wasAttributedTo": [
                    {
                        "@id": "https://orcid.org/0000-0003-2408-7588"
                    }
                ]
            }
        ]
    },
    {
        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/assertion",
        "@graph": [
            {
                "@id": "http://purl.org/nanopub/temp/np-f7dbc24c-dc54-4fc4-88ce-32ea5089daf9",
                "@type": [
                    "https://schema.org/Dataset"
                ],
                "https://w3id.org/np/snakemake/describesWorkflow": [
                    {
                        "@id": "https://w3id.org/np/RAOBjU_aTRgW5zb2MFGvZPAXBZegQRzVoUU-aSGQFpxh4"
                    }
                ],
                "https://w3id.org/np/snakemake/generatedAt": [
                    {
                        "@value": "2026-03-13T14:28:27.497122+00:00",
                        "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
                    }
                ],
                "https://w3id.org/np/snakemake/hasSummary": [
                    {
                        "@id": "http://purl.org/nanopub/temp/ws-0b516da4-630c-475e-9972-c8909bb16d4c"
                    }
                ],
                "https://w3id.org/np/snakemake/hasWorkflowRun": [
                    {
                        "@id": "http://purl.org/nanopub/temp/wr-1e3ea91f-7223-4d6e-a000-569fc443ac83"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/ws-0b516da4-630c-475e-9972-c8909bb16d4c",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowSummary"
                ],
                "https://w3id.org/np/snakemake/numberOfJobs": [
                    {
                        "@value": "8",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/numberOfResults": [
                    {
                        "@value": "2",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/numberOfRules": [
                    {
                        "@value": "6",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/wr-1e3ea91f-7223-4d6e-a000-569fc443ac83",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRun"
                ],
                "https://w3id.org/np/snakemake/configJSON": [
                    {
                        "@value": "{\"samples\": {\"A\": \"data/samples/A.fastq\", \"B\": \"data/samples/B.fastq\"}}"
                    }
                ],
                "https://w3id.org/np/snakemake/configfile": [
                    {
                        "@value": "config/config.yaml"
                    }
                ],
                "https://w3id.org/np/snakemake/dagSource": [
                    {
                        "@value": "Snakefile"
                    },
                    {
                        "@value": "config/config.yaml"
                    },
                    {
                        "@value": "envs/bcftools.yml"
                    },
                    {
                        "@value": "envs/bwa.yml"
                    },
                    {
                        "@value": "envs/matplotlib.yml"
                    },
                    {
                        "@value": "envs/samtools.yml"
                    },
                    {
                        "@value": "scripts/plot-positions.py"
                    },
                    {
                        "@value": "scripts/plot-quals.py"
                    }
                ],
                "https://w3id.org/np/snakemake/description": [
                    {
                        "@value": ""
                    }
                ],
                "https://w3id.org/np/snakemake/hasRule": [
                    {
                        "@id": "http://purl.org/nanopub/temp/rule-all"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/rule-bcftools_call"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/rule-bwa_mem"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/rule-plot_positions"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/rule-plot_quals"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/rule-samtools_index"
                    }
                ],
                "https://w3id.org/np/snakemake/includedSnakefile": [
                    {
                        "@value": "/home/meesters/Documents/Teaching/snakemake-hpc-teaching-material/snakemake-tutorial/Snakefile"
                    }
                ],
                "https://w3id.org/np/snakemake/mainSnakefile": [
                    {
                        "@value": "/home/meesters/Documents/Teaching/snakemake-hpc-teaching-material/snakemake-tutorial/Snakefile"
                    }
                ],
                "https://w3id.org/np/snakemake/workflowMetadataJSON": [
                    {
                        "@value": "{}"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/param-bwa_mem-1",
                "@type": [
                    "https://w3id.org/np/snakemake/Parameterization"
                ],
                "https://w3id.org/np/snakemake/parameterIndex": [
                    {
                        "@value": "1",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/parameterValue": [
                    {
                        "@value": "-R '@RG\\tID:{sample}\\tSM:{sample}'"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/param-bwa_mem-2",
                "@type": [
                    "https://w3id.org/np/snakemake/Parameterization"
                ],
                "https://w3id.org/np/snakemake/parameterIndex": [
                    {
                        "@value": "2",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/parameterValue": [
                    {
                        "@value": "samtools"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/param-bwa_mem-3",
                "@type": [
                    "https://w3id.org/np/snakemake/Parameterization"
                ],
                "https://w3id.org/np/snakemake/parameterIndex": [
                    {
                        "@value": "3",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/parameterValue": [
                    {
                        "@value": "coordinate"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/param-bwa_mem-4",
                "@type": [
                    "https://w3id.org/np/snakemake/Parameterization"
                ],
                "https://w3id.org/np/snakemake/parameterIndex": [
                    {
                        "@value": "4",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/parameterValue": [
                    {
                        "@value": ""
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/param-samtools_index-1",
                "@type": [
                    "https://w3id.org/np/snakemake/Parameterization"
                ],
                "https://w3id.org/np/snakemake/parameterIndex": [
                    {
                        "@value": "1",
                        "@type": "http://www.w3.org/2001/XMLSchema#integer"
                    }
                ],
                "https://w3id.org/np/snakemake/parameterValue": [
                    {
                        "@value": ""
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/rule-all",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRule"
                ],
                "https://w3id.org/np/snakemake/hasSoftwarePackage": [
                    {
                        "@value": "all"
                    }
                ],
                "https://w3id.org/np/snakemake/ruleName": [
                    {
                        "@value": "all"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/rule-bcftools_call",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRule"
                ],
                "https://w3id.org/np/snakemake/hasOutput": [
                    {
                        "@value": "calls/all.vcf"
                    }
                ],
                "https://w3id.org/np/snakemake/hasSoftwarePackage": [
                    {
                        "@value": "envs/bcftools.yml"
                    },
                    {
                        "@value": "shell"
                    }
                ],
                "https://w3id.org/np/snakemake/ruleName": [
                    {
                        "@value": "bcftools_call"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/rule-bwa_mem",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRule"
                ],
                "https://w3id.org/np/snakemake/hasOutput": [
                    {
                        "@value": "sorted_reads/A.bam"
                    },
                    {
                        "@value": "sorted_reads/B.bam"
                    },
                    {
                        "@value": "sorted_reads/{sample}.bam"
                    }
                ],
                "https://w3id.org/np/snakemake/hasParameterization": [
                    {
                        "@id": "http://purl.org/nanopub/temp/param-bwa_mem-1"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/param-bwa_mem-2"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/param-bwa_mem-3"
                    },
                    {
                        "@id": "http://purl.org/nanopub/temp/param-bwa_mem-4"
                    }
                ],
                "https://w3id.org/np/snakemake/hasSoftwarePackage": [
                    {
                        "@value": "envs/bwa.yml"
                    },
                    {
                        "@value": "v8.1.1/bio/bwa/mem"
                    }
                ],
                "https://w3id.org/np/snakemake/parametersJSON": [
                    {
                        "@value": "[\"-R '@RG\\\\tID:{sample}\\\\tSM:{sample}'\", \"samtools\", \"coordinate\", \"\"]"
                    }
                ],
                "https://w3id.org/np/snakemake/ruleName": [
                    {
                        "@value": "bwa_mem"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/rule-plot_positions",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRule"
                ],
                "https://w3id.org/np/snakemake/hasOutput": [
                    {
                        "@value": "calls/positions.png"
                    }
                ],
                "https://w3id.org/np/snakemake/hasSoftwarePackage": [
                    {
                        "@value": "envs/matplotlib.yml"
                    },
                    {
                        "@value": "scripts/plot-positions.py"
                    }
                ],
                "https://w3id.org/np/snakemake/ruleName": [
                    {
                        "@value": "plot_positions"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/rule-plot_quals",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRule"
                ],
                "https://w3id.org/np/snakemake/hasOutput": [
                    {
                        "@value": "calls/quals.png"
                    }
                ],
                "https://w3id.org/np/snakemake/hasSoftwarePackage": [
                    {
                        "@value": "envs/matplotlib.yml"
                    },
                    {
                        "@value": "scripts/plot-quals.py"
                    }
                ],
                "https://w3id.org/np/snakemake/ruleName": [
                    {
                        "@value": "plot_quals"
                    }
                ]
            },
            {
                "@id": "http://purl.org/nanopub/temp/rule-samtools_index",
                "@type": [
                    "https://w3id.org/np/snakemake/WorkflowRule"
                ],
                "https://w3id.org/np/snakemake/hasOutput": [
                    {
                        "@value": "sorted_reads/A.bam.bai"
                    },
                    {
                        "@value": "sorted_reads/B.bam.bai"
                    },
                    {
                        "@value": "sorted_reads/{sample}.bam.bai"
                    }
                ],
                "https://w3id.org/np/snakemake/hasParameterization": [
                    {
                        "@id": "http://purl.org/nanopub/temp/param-samtools_index-1"
                    }
                ],
                "https://w3id.org/np/snakemake/hasSoftwarePackage": [
                    {
                        "@value": "envs/samtools.yml"
                    },
                    {
                        "@value": "v5.7.0/bio/samtools/index"
                    }
                ],
                "https://w3id.org/np/snakemake/parametersJSON": [
                    {
                        "@value": "[\"\"]"
                    }
                ],
                "https://w3id.org/np/snakemake/ruleName": [
                    {
                        "@value": "samtools_index"
                    }
                ]
            }
        ]
    },
    {
        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/Head",
        "@graph": [
            {
                "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk",
                "http://www.nanopub.org/nschema#hasAssertion": [
                    {
                        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/assertion"
                    }
                ],
                "http://www.nanopub.org/nschema#hasProvenance": [
                    {
                        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/provenance"
                    }
                ],
                "http://www.nanopub.org/nschema#hasPublicationInfo": [
                    {
                        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/pubinfo"
                    }
                ],
                "@type": [
                    "http://www.nanopub.org/nschema#Nanopublication"
                ]
            }
        ]
    },
    {
        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/pubinfo",
        "@graph": [
            {
                "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk",
                "http://www.w3.org/ns/prov#generatedAtTime": [
                    {
                        "@value": "2026-03-13T15:28:27.526317",
                        "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
                    }
                ],
                "http://www.w3.org/ns/prov#wasAttributedTo": [
                    {
                        "@id": "https://orcid.org/0000-0003-2408-7588"
                    }
                ]
            },
            {
                "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/sig",
                "http://purl.org/nanopub/x/hasAlgorithm": [
                    {
                        "@value": "RSA"
                    }
                ],
                "http://purl.org/nanopub/x/hasPublicKey": [
                    {
                        "@value": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB"
                    }
                ],
                "http://purl.org/nanopub/x/hasSignature": [
                    {
                        "@value": "KMngg3UHe2KcXwu6O+8dxqaJs3xFoUZz1XlELpqZ5TqBBAVu+yyQloTd34ks9eW9HiqqQJg0I1F9kZswQI8cLolTCP5yAtPyzC4JVJhncvP3+jR8KJxiB6V45H0+6v+pi8i1Oe0XVn3JxRyidsszCEo+XX+q1wx+2S7gN6r2mjMj9MrH7L6vvVevzsgYmdKoYBbCNjvabNtyCVX7mwFQ3hRJRKV8w4ZhfiJZn5funeVzT8UPWMdMxzl7Prg2DgpZKHSiU5vdj+vwZxn/NCACw3S3vLaZE6+ijJ8Q39Dc78rRKrrxUF0/3RfKPsuNnqWav3PbUuN1JfgZ/Ki9w0d22g=="
                    }
                ],
                "http://purl.org/nanopub/x/hasSignatureTarget": [
                    {
                        "@id": "https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk"
                    }
                ],
                "http://purl.org/nanopub/x/signedBy": [
                    {
                        "@id": "https://orcid.org/0000-0003-2408-7588"
                    }
                ]
            }
        ]
    }
]