@prefix dcterms: .
@prefix np: .
@prefix npx: .
@prefix ns1: .
@prefix orcid: .
@prefix prov: .
@prefix rdfs: .
@prefix schema: .
@prefix sub: .
@prefix this: .
@prefix xsd: .
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.yml";
schema:text """samples: samples.csv
ref:
species: \"Drosophila melanogaster\"
genome: \"\"
annotation: \"\"
accession: \"GCF_000001215.4\"
ensembl_species: \"\" # e.g., \"homo_sapiens\"
build: \"\" # e.g., \"GRCh38\"
release: \"\" # e.g., \"105\"
read_filter:
min_length: 200
minimap2:
index_opts: \"\"
opts: \"\"
maximum_secondary: 100
secondary_score_ratio: 1.0
samtools:
samtobam_opts: \"-b\"
bamsort_opts: \"\"
bamindex_opts: \"\"
bamstats_opts: \"\"
quant:
salmon_libtype: \"U\"
deseq2:
fit_type: \"\"
design_factors:
- \"condition\"
lfc_null: 1.0
alt_hypothesis: \"greaterAbs\"
point_width: 20
mincount: 10
alpha: 0.05
threshold_plot: 10
colormap: \"Blues\"
figtype: \"png\"
batch_effect:
- \"\"
isoform_analysis:
FLAIR: true
qscore: 1
exp_thresh: 10
col_opts: \"--annotation_reliant generate --generate_map --stringent\"
protein_annotation:
lambda: false
uniref: \"https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz\"
num_matches: 3""" .
sub:dataset a schema:Dataset;
ns1:describesWorkflow "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
ns1:description """
This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology.
First a transcriptome FASTA is constructed using gffread. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2.
Next quantification is performed using salmon before normalization and differential expression analysis are conducted by PyDESeq2.
The workflow can optionally analyze splice-isoforms through integrating the FLAIR workflow.
Additionaly, NanoPlot is employed to analyze initial sequencing data and QualiMap is used to evaluate mapping results.
""";
ns1:generatedAt "2026-04-17T13:04:00.726901+00:00"^^xsd:dateTime;
ns1:hasConfigurationSection sub:workflow-configuration .
sub:workflow-configuration rdfs:label "from workflow configuration";
ns1:hasConfigurationFile sub:config-1 .
}
sub:provenance {
sub:assertion prov:generatedAtTime "2026-04-17T15:04:01.867078"^^xsd:dateTime;
prov:wasAttributedTo orcid:0000-0003-2408-7588 .
}
sub:pubinfo {
this: dcterms:created "2026-04-17T13:04:00.726901+00:00"^^xsd:dateTime;
dcterms:creator orcid:0000-0003-2408-7588;
npx:hasNanopubType schema:Dataset;
npx:signedBy orcid:0000-0003-2408-7588;
rdfs:label "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE";
prov:generatedAtTime "2026-04-17T15:04:01.867078"^^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 "OyzfUSPjlXJ9aurpYvgNiMGmXg4nl9o/s8+erXi20wtEi82FRRnfCaAiveUZd4TGgx3AzkkbPIPT7Ay8daCQo94EhED+abz18be/L6DV+Q/BWt9oTmvbafTw/g3N+JtQd3BnpOFZ707YefMEfMKRufZSZ+QL/Pov4DVtisTd/BWth2UwFzbK+peWJudkWpuudQS1Mog8zDUvWF2Pdlr3+37ukiz3Ly5QWo460WprpQixfLJtCo/Zi+cIFk1IRWirAksco/FdygO5h4QC6OM9IXmqG0zt+1enKKGW7DpUdquKLarswirPVdyUWQSd27kZTeV50G9UpiFdq1EWIElHFg==";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0000-0003-2408-7588 .
}