. . . . "config.yml" . "samples: samples.csv\n\nref:\n species: \"Drosophila melanogaster\"\n genome: \"\"\n annotation: \"\"\n accession: \"GCF_000001215.4\"\n ensembl_species: \"\" # e.g., \"homo_sapiens\"\n build: \"\" # e.g., \"GRCh38\"\n release: \"\" # e.g., \"105\"\n\nread_filter:\n min_length: 200\n\nminimap2:\n index_opts: \"\"\n opts: \"\"\n maximum_secondary: 100\n secondary_score_ratio: 1.0\n\nsamtools:\n samtobam_opts: \"-b\"\n bamsort_opts: \"\"\n bamindex_opts: \"\"\n bamstats_opts: \"\"\n\nquant:\n salmon_libtype: \"U\"\n\ndeseq2:\n fit_type: \"\"\n design_factors:\n - \"condition\"\n lfc_null: 1.0\n alt_hypothesis: \"greaterAbs\"\n point_width: 20\n mincount: 10\n alpha: 0.05\n threshold_plot: 10\n colormap: \"Blues\"\n figtype: \"png\"\n batch_effect:\n - \"\"\n\nisoform_analysis:\n FLAIR: true\n qscore: 1\n exp_thresh: 10\n col_opts: \"--annotation_reliant generate --generate_map --stringent\"\n\nprotein_annotation:\n lambda: false\n uniref: \"https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz\"\n num_matches: 3" . . "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" . "This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology.\nFirst 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].\nNext 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].\nThe workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow.\nAdditionaly, 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." . "2026-05-05T18:00:57.134252+00:00"^^ . . . "sorted_alignments/{sample}_sorted.bam" . "QC/qualimap/{sample}" . "github.com/snakemake/snakemake-wrappers/bio/qualimap/bamqc/environment.yaml@v4.4.0" . "QC/qualimap/{sample}" . "qualimap/{sample}/qualimapReport.html" . "python>=3.12.4" . "sorted_alignments/{sample}_sorted.bam" . "sorted_alignments/{sample}_sorted.bam.bai" . "github.com/snakemake/snakemake-wrappers/bio/samtools/index/environment.yaml@v7.6.0" . "alignments/{sample}.bam" . "sorted_alignments/{sample}_sorted.bam" . "github.com/snakemake/snakemake-wrappers/bio/samtools/sort/environment.yaml@v7.6.0" . "alignments/{sample}.bam" . "QC/bamstats/{sample}.txt" . "github.com/snakemake/snakemake-wrappers/bio/samtools/stats/environment.yaml@v3.13.4" . "sorted_alignments/{sample}_sorted.bam" . "sorted_alignments/{sample}_sorted.bam.bai" . "iso_analysis/beds/{sample}.bed" . "flair=2.0.0" . "references/genomic.fa" . "index/flair_genome_index.mmi" . "github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0" . "transcriptome/corrected_transcriptome.fa" . "index/transcriptome_index.mmi" . "github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0" . "iso_analysis/beds/barcode10.bed" . "iso_analysis/beds/barcode11.bed" . "iso_analysis/beds/barcode12.bed" . "iso_analysis/beds/barcode13.bed" . "iso_analysis/beds/barcode15.bed" . "iso_analysis/beds/barcode16.bed" . "iso_analysis/beds/all_samples.bed" . "python>=3.12.4" . "transcriptome/transcriptome.fa" . "transcriptome/corrected_transcriptome.fa" . "gffread>=0.12.7" . "alignments/{sample}.bam" . "transcriptome/corrected_transcriptome.fa" . "counts/{sample}_salmon/quant.sf" . "salmon>=1.10.3" . "de_analysis/all.rds" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_MA_plot.svg" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_count_heatmap.svg" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_dispersion_plot.svg" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_sample_heatmap.svg" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_top_count_heatmap.svg" . "bioconductor-deseq2 =1.46.0" . "r-ashr =2.2_63" . "r-pheatmap" . "r-rcolorbrewer" . "r-stringr =1.5.1" . "/fshpc/meesters/projects/snakemake-workflows/rna-longseq-de-isoform/config/demo/samples.csv" . "merged/all_counts_gene.tsv" . "de_analysis/all.rds" . "de_analysis/normcounts.tsv" . "bioconductor-deseq2 =1.46.0" . "r-ashr =2.2_63" . "r-pheatmap" . "r-rcolorbrewer" . "r-stringr =1.5.1" . "references/ensembl_annotation.gff3" . "github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-annotation/environment.yaml@v7.5.0" . "references/ensembl_genome.fa" . "github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-sequence/environment.yaml@v7.5.0" . "references/ncbi_dataset_annotation.zip" . "ncbi-datasets-cli>=18.14.0" . "unzip>=6.0.0" . "references/ncbi_dataset_genome.zip" . "ncbi-datasets-cli>=18.14.0" . "unzip>=6.0.0" . "filter/{sample}_filtered.fq" . "biopython >=1.84" . "pandas>=2.2.2" . "python>=3.12.4" . "filter/barcode10_filtered.fq" . "filter/barcode11_filtered.fq" . "filter/barcode12_filtered.fq" . "filter/barcode13_filtered.fq" . "filter/barcode15_filtered.fq" . "filter/barcode16_filtered.fq" . "index/flair_genome_index.mmi" . "references/genomic.fa" . "iso_analysis/align/flair.bam" . "iso_analysis/align/flair.bam.bai" . "iso_analysis/align/flair.bed" . "flair=2.0.0" . "filter/barcode10_filtered.fq" . "filter/barcode11_filtered.fq" . "filter/barcode12_filtered.fq" . "filter/barcode13_filtered.fq" . "filter/barcode15_filtered.fq" . "filter/barcode16_filtered.fq" . "iso_analysis/align/flair_all_corrected.bed" . "references/genomic.fa" . "references/standardized_genomic.gtf" . "iso_analysis/collapse/flair.isoforms.bed" . "iso_analysis/collapse/flair.isoforms.fa" . "flair=2.0.0" . "iso_analysis/align/flair.bed" . "references/genomic.fa" . "references/standardized_genomic.gtf" . "iso_analysis/align/flair_all_corrected.bed" . "flair=2.0.0" . "iso_analysis/quantify/flair.counts.tsv" . "iso_analysis/diffexp/genes_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf" . "iso_analysis/diffexp/genes_deseq2_{condition_value1}_v_{condition_value2}.tsv" . "iso_analysis/diffexp/isoforms_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf" . "iso_analysis/diffexp/isoforms_deseq2_{condition_value1}_v_{condition_value2}.tsv" . "iso_analysis/diffexp/isoforms_drimseq_{condition_value1}_v_{condition_value2}.tsv" . "flair=2.0.0" . "iso_analysis/collapse/flair.isoforms.bed" . "iso_analysis/quantify/flair.counts.tsv" . "iso_analysis/plots" . "flair=2.0.0" . "iso_analysis/collapse/flair.isoforms.bed" . "iso_analysis/collapse/flair.isoforms.fa" . "iso_analysis/reads_manifest.tsv" . "iso_analysis/quantify/flair.counts.tsv" . "flair=2.0.0" . "de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv" . "transcriptome/corrected_transcriptome.fa" . "protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa" . "biopython >=1.84" . "pandas>=2.2.2" . "python>=3.12.4" . "references/genomic.fa" . "references/standardized_genomic.gff" . "references/genomic.fa.fai" . "transcriptome/transcriptome.fa" . "gffread>=0.12.7" . "references/genomic.gff" . "ncbi-datasets-cli>=18.14.0" . "unzip>=6.0.0" . "references/genomic.fa" . "ncbi-datasets-cli>=18.14.0" . "unzip>=6.0.0" . "protein_annotation/index/UniRef.lba.gz" . "wget>=1.21.4" . "protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8" . "protein_annotation/proteins_{factor}_{prop_a}_vs_{prop_b}.csv" . "biopython >=1.84" . "pandas>=2.2.2" . "python>=3.12.4" . "references/standardized_genomic.gff" . "references/standardized_genomic.gtf" . "gffread>=0.12.7" . "iso_analysis/plots" . "iso_analysis/report/isoforms" . "iso_analysis/report/usage" . "python>=3.12.4" . "protein_annotation/index/UniRef.lba.gz" . "protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa" . "protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8" . "lambda>=3.1.0" . "filter/{sample}_filtered.fq" . "index/transcriptome_index.mmi" . "alignments/{sample}.sam" . "github.com/snakemake/snakemake-wrappers/bio/minimap2/aligner/environment.yaml@v7.6.0" . "counts/barcode10_salmon/quant.sf" . "counts/barcode11_salmon/quant.sf" . "counts/barcode12_salmon/quant.sf" . "counts/barcode13_salmon/quant.sf" . "counts/barcode15_salmon/quant.sf" . "counts/barcode16_salmon/quant.sf" . "merged/all_counts.tsv" . "pandas>=2.2.2" . "python>=3.12.4" . "de_analysis/all.rds" . "de_analysis/pca_{variable}.svg" . "bioconductor-deseq2 =1.46.0" . "r-ashr =2.2_63" . "r-pheatmap" . "r-rcolorbrewer" . "r-stringr =1.5.1" . "iso_analysis/reads_manifest.tsv" . "pandas>=2.2.2" . "python>=3.12.4" . "alignments/{sample}.sam" . "alignments/{sample}.bam" . "github.com/snakemake/snakemake-wrappers/bio/samtools/view/environment.yaml@v7.6.0" . "NanoPlot/{sample}/NanoPlot-report.html" . "nanoplot" . "references/genomic.gff" . "references/standardized_genomic.gff" . "agat>=1.4.0" . "/lustre/project/nhr-zdvhpc/dtest/raw/barcode10.fastq.gz" . "/lustre/project/nhr-zdvhpc/dtest/raw/barcode11.fastq.gz" . "/lustre/project/nhr-zdvhpc/dtest/raw/barcode12.fastq.gz" . "/lustre/project/nhr-zdvhpc/dtest/raw/barcode13.fastq.gz" . "/lustre/project/nhr-zdvhpc/dtest/raw/barcode15.fastq.gz" . "/lustre/project/nhr-zdvhpc/dtest/raw/barcode16.fastq.gz" . "NanoPlot/NanoPlot-report.html" . "nanoplot" . "merged/all_counts.tsv" . "references/standardized_genomic.gff" . "merged/all_counts_gene.tsv" . "merged/transcriptid_to_gene_plot.svg" . "anndata=0.10.8" . "bioinfokit" . "pydeseq2=0.4.10" . "seaborn>=0.13.2" . "from workflow configuration" . . "workflow rules" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "2026-05-05T20:00:58.808466+02:00"^^ . . "2026-05-05T18:00:57.134252+00:00"^^ . . . . "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" . "2026-05-05T20:00:58.808466+02:00"^^ . . "RSA" . "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB" . "Vo0CJzbsFqEdqAPghIWU050/pHH7rTp4FQqEfXT+LS5vLwC1r2kYGHEcsIDA5JOERzke4j4QwAEtxwQdpHdmR/pA0LuXESROtDQhD46+zqjwHHsVLilSjno9aEc/DE9lVgIjrDEhd1wU0GtyuHdCv7iRV5BlnK1Xy5PNP5WtVTPNIt76T7gKAsuLNlzXZgJwSj37+eqmkcC8cfVszoSmXAIr8LikPPlBykP87S8oo2mxWvOZ805oYIriSHSTEWhXjAKLswmLSbkd2hXZiZLczSVJkdGviK91oY5p0p1zXsZZpusgywy0XeX93QOta8K2wGxmT/Y7w3IFk3MqH/5jvw==" . . .