Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-04-17T14:23:10.537850+00:00
creator: https://orcid.org/0000-0003-2408-7588
has nanopub type: Dataset
signed by: https://orcid.org/0000-0003-2408-7588
generated at time: 2026-04-17T16:23:11.855128
was attributed to: https://orcid.org/0000-0003-2408-7588

config-1
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

dataset
type: Dataset
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 [https://github.com/gpertea/gffread]. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2]. Next quantification is performed using salmon [https://github.com/COMBINE-lab/salmon] before normalization and differential expression analysis are conducted by PyDESeq2 [https://github.com/owkin/PyDESeq2]. The workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow. Additionaly, NanoPlot [https://github.com/wdecoster/NanoPlot] is employed to analyze initial sequencing data and QualiMap [https://github.com/EagleGenomics-cookbooks/QualiMap] is used to evaluate mapping results.
generated at: 2026-04-17T14:23:10.537850+00:00
has configuration section: from workflow configuration
has job: job-1-alignment qa
has job: job-10-alignment qa report
has job: job-11-alignment qa report
has job: job-12-alignment qa report
has job: job-13-bam sort
has job: job-14-bam sort
has job: job-15-bam sort
has job: job-16-bam sort
has job: job-17-bam sort
has job: job-18-bam sort
has job: job-19-bam stats
has job: job-2-alignment qa
has job: job-20-bam stats
has job: job-21-bam stats
has job: job-22-bam stats
has job: job-23-bam stats
has job: job-24-bam stats
has job: job-25-build flair genome index
has job: job-26-build minimap index
has job: job-27-correct transcriptome
has job: job-28-count reads
has job: job-29-count reads
has job: job-3-alignment qa
has job: job-30-count reads
has job: job-31-count reads
has job: job-32-count reads
has job: job-33-count reads
has job: job-34-deseq2
has job: job-35-deseq2 init
has job: job-36-download ncbi annotation
has job: job-37-download ncbi genome
has job: job-38-filter reads
has job: job-39-filter reads
has job: job-4-alignment qa
has job: job-40-filter reads
has job: job-41-filter reads
has job: job-42-filter reads
has job: job-43-filter reads
has job: job-44-flair align
has job: job-45-flair collapse
has job: job-46-flair correct
has job: job-47-flair diffexp
has job: job-48-flair plot isoforms
has job: job-49-flair quantify
has job: job-5-alignment qa
has job: job-50-genome to transcriptome
has job: job-51-get annotation
has job: job-52-get genome
has job: job-53-gff to gtf
has job: job-54-iso analysis report
has job: job-55-map reads
has job: job-56-map reads
has job: job-57-map reads
has job: job-58-map reads
has job: job-59-map reads
has job: job-6-alignment qa
has job: job-60-map reads
has job: job-61-merge read counts
has job: job-62-reads manifest
has job: job-63-sam to bam
has job: job-64-sam to bam
has job: job-65-sam to bam
has job: job-66-sam to bam
has job: job-67-sam to bam
has job: job-68-sam to bam
has job: job-69-sample qa plot
has job: job-7-alignment qa report
has job: job-70-sample qa plot
has job: job-71-sample qa plot
has job: job-72-sample qa plot
has job: job-73-sample qa plot
has job: job-74-sample qa plot
has job: job-75-standardize gff
has job: job-76-total sample qa plot
has job: job-77-transcriptid to gene
has job: job-8-alignment qa report

job-1-alignment qa
type: WorkflowJob
rule name: alignment_qa

job-10-alignment qa report
type: WorkflowJob
rule name: alignment_qa_report

job-11-alignment qa report
type: WorkflowJob
rule name: alignment_qa_report

job-12-alignment qa report
type: WorkflowJob
rule name: alignment_qa_report

job-13-bam sort
type: WorkflowJob
rule name: bam_sort

job-14-bam sort
type: WorkflowJob
rule name: bam_sort

job-15-bam sort
type: WorkflowJob
rule name: bam_sort

job-16-bam sort
type: WorkflowJob
rule name: bam_sort

job-17-bam sort
type: WorkflowJob
rule name: bam_sort

job-18-bam sort
type: WorkflowJob
rule name: bam_sort

job-19-bam stats
type: WorkflowJob
rule name: bam_stats

job-2-alignment qa
type: WorkflowJob
rule name: alignment_qa

job-20-bam stats
type: WorkflowJob
rule name: bam_stats

job-21-bam stats
type: WorkflowJob
rule name: bam_stats

job-22-bam stats
type: WorkflowJob
rule name: bam_stats

job-23-bam stats
type: WorkflowJob
rule name: bam_stats

job-24-bam stats
type: WorkflowJob
rule name: bam_stats

job-25-build flair genome index
type: WorkflowJob
rule name: build_flair_genome_index

job-26-build minimap index
type: WorkflowJob
rule name: build_minimap_index

job-27-correct transcriptome
type: WorkflowJob
rule name: correct_transcriptome

job-28-count reads
type: WorkflowJob
rule name: count_reads

job-29-count reads
type: WorkflowJob
rule name: count_reads

job-3-alignment qa
type: WorkflowJob
rule name: alignment_qa

job-30-count reads
type: WorkflowJob
rule name: count_reads

job-31-count reads
type: WorkflowJob
rule name: count_reads

job-32-count reads
type: WorkflowJob
rule name: count_reads

job-33-count reads
type: WorkflowJob
rule name: count_reads

job-34-deseq2
type: WorkflowJob
rule name: deseq2

job-35-deseq2 init
type: WorkflowJob
rule name: deseq2_init

job-36-download ncbi annotation
type: WorkflowJob
rule name: download_ncbi_annotation

job-37-download ncbi genome
type: WorkflowJob
rule name: download_ncbi_genome

job-38-filter reads
type: WorkflowJob
rule name: filter_reads

job-39-filter reads
type: WorkflowJob
rule name: filter_reads

job-4-alignment qa
type: WorkflowJob
rule name: alignment_qa

job-40-filter reads
type: WorkflowJob
rule name: filter_reads

job-41-filter reads
type: WorkflowJob
rule name: filter_reads

job-42-filter reads
type: WorkflowJob
rule name: filter_reads

job-43-filter reads
type: WorkflowJob
rule name: filter_reads

job-44-flair align
type: WorkflowJob
rule name: flair_align

job-45-flair collapse
type: WorkflowJob
rule name: flair_collapse

job-46-flair correct
type: WorkflowJob
rule name: flair_correct

job-47-flair diffexp
type: WorkflowJob
rule name: flair_diffexp

job-48-flair plot isoforms
type: WorkflowJob
rule name: flair_plot_isoforms

job-49-flair quantify
type: WorkflowJob
rule name: flair_quantify

job-5-alignment qa
type: WorkflowJob
rule name: alignment_qa

job-50-genome to transcriptome
type: WorkflowJob
rule name: genome_to_transcriptome

job-51-get annotation
type: WorkflowJob
rule name: get_annotation

job-52-get genome
type: WorkflowJob
rule name: get_genome

job-53-gff to gtf
type: WorkflowJob
rule name: gff_to_gtf

job-54-iso analysis report
type: WorkflowJob
rule name: iso_analysis_report

job-55-map reads
type: WorkflowJob
rule name: map_reads

job-56-map reads
type: WorkflowJob
rule name: map_reads

job-57-map reads
type: WorkflowJob
rule name: map_reads

job-58-map reads
type: WorkflowJob
rule name: map_reads

job-59-map reads
type: WorkflowJob
rule name: map_reads

job-6-alignment qa
type: WorkflowJob
rule name: alignment_qa

job-60-map reads
type: WorkflowJob
rule name: map_reads

job-61-merge read counts
type: WorkflowJob
rule name: merge_read_counts

job-62-reads manifest
type: WorkflowJob
rule name: reads_manifest

job-63-sam to bam
type: WorkflowJob
rule name: sam_to_bam

job-64-sam to bam
type: WorkflowJob
rule name: sam_to_bam

job-65-sam to bam
type: WorkflowJob
rule name: sam_to_bam

job-66-sam to bam
type: WorkflowJob
rule name: sam_to_bam

job-67-sam to bam
type: WorkflowJob
rule name: sam_to_bam

job-68-sam to bam
type: WorkflowJob
rule name: sam_to_bam

job-69-sample qa plot
type: WorkflowJob
rule name: sample_qa_plot

job-7-alignment qa report
type: WorkflowJob
rule name: alignment_qa_report

job-70-sample qa plot
type: WorkflowJob
rule name: sample_qa_plot

job-71-sample qa plot
type: WorkflowJob
rule name: sample_qa_plot

job-72-sample qa plot
type: WorkflowJob
rule name: sample_qa_plot

job-73-sample qa plot
type: WorkflowJob
rule name: sample_qa_plot

job-74-sample qa plot
type: WorkflowJob
rule name: sample_qa_plot

job-75-standardize gff
type: WorkflowJob
rule name: standardize_gff

job-76-total sample qa plot
type: WorkflowJob
rule name: total_sample_qa_plot

job-77-transcriptid to gene
type: WorkflowJob
rule name: transcriptid_to_gene

job-8-alignment qa report
type: WorkflowJob
rule name: alignment_qa_report

job-9-alignment qa report
type: WorkflowJob
rule name: alignment_qa_report

from workflow configuration
has configuration file: config-1

assertion
generated at time: 2026-04-17T16:23:11.855128
was attributed to: https://orcid.org/0000-0003-2408-7588

sig
has algorithm: RSA
signed by: https://orcid.org/0000-0003-2408-7588