Christian Meesters RSA MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCKyTtRc5W2LD8SIQhd+T7IOhgr4GinEVpynNUiUppNi1Yvdo+qHljDplzsXlxc4pPwEB2+/RBYT75rMeD/VrV12s5Aq9t5XalDFKnxPE1vFN4P3dINAOq8ikc1yzU0fpJpz09+tefHG+Zk1Mz90PnLWLCs30wM6Iq6hI5NHmjklQIDAQAB Christian Meesters RSA MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQC+DVJTSCzdJUJMzlwRfb2Qm2NZpuZ932RpVliWxMAhmZ6ZkeeibmJlW/Z0q51YkFArJIWbJ0f7rLQWM5epuZV4I5cjMqepOWGey6LrPolMs8lI9dJf9zW9lJsneV+py3U8WsrB6mg//pkEeXnVDd+WscADyXJ5EeLwoZjCkPn8/QIDAQAB I am a sceptic of web applications and reproducibility. However, knowing some participants of this hackathon personally, I gained some trust. interesting summary for ligand screening and validation corner stone of data analysis config.yml 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 RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE 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. 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 config.yml 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 RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE 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. 2026-05-05T15:42:06.149516+00:00 sorted_alignments/{sample}_sorted.bam QC/qualimap/{sample} github.com/snakemake/snakemake-wrappers/bio/qualimap/bamqc/environment.yaml@v4.4.0 v4.4.0 QC/qualimap/{sample} qualimap/{sample}/qualimapReport.html ../envs/base.yml sorted_alignments/{sample}_sorted.bam sorted_alignments/{sample}_sorted.bam.bai github.com/snakemake/snakemake-wrappers/bio/samtools/index/environment.yaml@v7.6.0 v7.6.0 alignments/{sample}.bam sorted_alignments/{sample}_sorted.bam github.com/snakemake/snakemake-wrappers/bio/samtools/sort/environment.yaml@v7.6.0 v7.6.0 alignments/{sample}.bam QC/bamstats/{sample}.txt github.com/snakemake/snakemake-wrappers/bio/samtools/stats/environment.yaml@v3.13.4 v3.13.4 sorted_alignments/{sample}_sorted.bam sorted_alignments/{sample}_sorted.bam.bai iso_analysis/beds/{sample}.bed ../envs/flair.yml references/genomic.fa index/flair_genome_index.mmi github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0 v7.6.0 transcriptome/corrected_transcriptome.fa index/transcriptome_index.mmi github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0 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 ../envs/base.yml transcriptome/transcriptome.fa transcriptome/corrected_transcriptome.fa ../envs/gffread.yml alignments/{sample}.bam transcriptome/corrected_transcriptome.fa counts/{sample}_salmon/quant.sf ../envs/salmon.yml 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 ../envs/deseq2.yml /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 ../envs/deseq2.yml references/ensembl_annotation.gff3 github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-annotation/environment.yaml@v7.5.0 v7.5.0 references/ensembl_genome.fa github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-sequence/environment.yaml@v7.5.0 v7.5.0 references/ncbi_dataset_annotation.zip ../envs/reference.yml references/ncbi_dataset_genome.zip ../envs/reference.yml <function <lambda> at 0x7fcf6a1dce00> filter/{sample}_filtered.fq ../envs/biopython.yml 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 ../envs/flair.yml 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 ../envs/flair.yml iso_analysis/align/flair.bed references/genomic.fa references/standardized_genomic.gtf iso_analysis/align/flair_all_corrected.bed ../envs/flair.yml 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 ../envs/flair.yml <function <lambda> at 0x7fcf6a1df2e0> iso_analysis/collapse/flair.isoforms.bed iso_analysis/quantify/flair.counts.tsv iso_analysis/plots ../envs/flair.yml iso_analysis/collapse/flair.isoforms.bed iso_analysis/collapse/flair.isoforms.fa iso_analysis/reads_manifest.tsv iso_analysis/quantify/flair.counts.tsv ../envs/flair.yml 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 ../envs/biopython.yml references/genomic.fa references/standardized_genomic.gff references/genomic.fa.fai transcriptome/transcriptome.fa ../envs/gffread.yml <function <lambda> at 0x7fcf6a394cc0> references/genomic.gff ../envs/reference.yml <function <lambda> at 0x7fcf6a394d60> references/genomic.fa ../envs/reference.yml protein_annotation/index/UniRef.lba.gz ../envs/wget.yml protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8 protein_annotation/proteins_{factor}_{prop_a}_vs_{prop_b}.csv ../envs/biopython.yml references/standardized_genomic.gff references/standardized_genomic.gtf ../envs/gffread.yml iso_analysis/plots iso_analysis/report/isoforms iso_analysis/report/usage ../envs/base.yml 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 ../envs/lambda3.yml filter/{sample}_filtered.fq index/transcriptome_index.mmi alignments/{sample}.sam github.com/snakemake/snakemake-wrappers/bio/minimap2/aligner/environment.yaml@v7.6.0 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 ../envs/pandas.yml de_analysis/all.rds de_analysis/pca_{variable}.svg ../envs/deseq2.yml iso_analysis/reads_manifest.tsv ../envs/pandas.yml alignments/{sample}.sam alignments/{sample}.bam github.com/snakemake/snakemake-wrappers/bio/samtools/view/environment.yaml@v7.6.0 v7.6.0 <function <lambda> at 0x7fcf6a397ba0> NanoPlot/{sample}/NanoPlot-report.html ../envs/nanoplot.yml references/genomic.gff references/standardized_genomic.gff ../envs/agat.yml /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 ../envs/nanoplot.yml merged/all_counts.tsv references/standardized_genomic.gff merged/all_counts_gene.tsv merged/transcriptid_to_gene_plot.svg ../envs/pydeseq2.yml from workflow configuration workflow rules A gentle introduction to Nanopubs Nanopub 101 Welcome! config.yml 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 RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE 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. 2026-04-17T15:19:46.851430+00:00 QC/qualimap/barcode10 alignment_qa qualimap/barcode13/qualimapReport.html alignment_qa_report qualimap/barcode15/qualimapReport.html alignment_qa_report qualimap/barcode16/qualimapReport.html alignment_qa_report sorted_alignments/barcode10_sorted.bam bam_sort sorted_alignments/barcode11_sorted.bam bam_sort sorted_alignments/barcode12_sorted.bam bam_sort sorted_alignments/barcode13_sorted.bam bam_sort sorted_alignments/barcode15_sorted.bam bam_sort sorted_alignments/barcode16_sorted.bam bam_sort QC/bamstats/barcode10.txt bam_stats QC/qualimap/barcode11 alignment_qa QC/bamstats/barcode11.txt bam_stats QC/bamstats/barcode12.txt bam_stats QC/bamstats/barcode13.txt bam_stats QC/bamstats/barcode15.txt bam_stats QC/bamstats/barcode16.txt bam_stats index/flair_genome_index.mmi build_flair_genome_index index/transcriptome_index.mmi build_minimap_index transcriptome/corrected_transcriptome.fa correct_transcriptome counts/barcode10_salmon/quant.sf count_reads counts/barcode11_salmon/quant.sf count_reads QC/qualimap/barcode12 alignment_qa counts/barcode12_salmon/quant.sf count_reads counts/barcode13_salmon/quant.sf count_reads counts/barcode15_salmon/quant.sf count_reads counts/barcode16_salmon/quant.sf count_reads de_analysis/condition_wt_vs_mt_MA_plot.svg de_analysis/condition_wt_vs_mt_count_heatmap.svg de_analysis/condition_wt_vs_mt_dispersion_plot.svg de_analysis/condition_wt_vs_mt_l2fc.tsv de_analysis/condition_wt_vs_mt_sample_heatmap.svg de_analysis/condition_wt_vs_mt_top_count_heatmap.svg deseq2 de_analysis/all.rds de_analysis/normcounts.tsv deseq2_init references/ncbi_dataset_annotation.zip download_ncbi_annotation references/ncbi_dataset_genome.zip download_ncbi_genome filter/barcode10_filtered.fq filter_reads filter/barcode11_filtered.fq filter_reads QC/qualimap/barcode13 alignment_qa filter/barcode12_filtered.fq filter_reads filter/barcode13_filtered.fq filter_reads filter/barcode15_filtered.fq filter_reads filter/barcode16_filtered.fq filter_reads iso_analysis/align/flair.bam iso_analysis/align/flair.bam.bai iso_analysis/align/flair.bed flair_align iso_analysis/collapse/flair.isoforms.bed iso_analysis/collapse/flair.isoforms.fa flair_collapse iso_analysis/align/flair_all_corrected.bed flair_correct iso_analysis/diffexp/genes_deseq2_QCplots_wt_v_mt.pdf iso_analysis/diffexp/genes_deseq2_wt_v_mt.tsv iso_analysis/diffexp/isoforms_deseq2_QCplots_wt_v_mt.pdf iso_analysis/diffexp/isoforms_deseq2_wt_v_mt.tsv iso_analysis/diffexp/isoforms_drimseq_wt_v_mt.tsv flair_diffexp iso_analysis/plots flair_plot_isoforms iso_analysis/quantify/flair.counts.tsv flair_quantify QC/qualimap/barcode15 alignment_qa references/genomic.fa.fai transcriptome/transcriptome.fa genome_to_transcriptome references/genomic.gff get_annotation references/genomic.fa get_genome references/standardized_genomic.gtf gff_to_gtf iso_analysis/report/isoforms iso_analysis/report/usage iso_analysis_report alignments/barcode10.sam map_reads alignments/barcode11.sam map_reads alignments/barcode12.sam map_reads alignments/barcode13.sam map_reads alignments/barcode15.sam map_reads QC/qualimap/barcode16 alignment_qa alignments/barcode16.sam map_reads merged/all_counts.tsv merge_read_counts iso_analysis/reads_manifest.tsv reads_manifest alignments/barcode10.bam sam_to_bam alignments/barcode11.bam sam_to_bam alignments/barcode12.bam sam_to_bam alignments/barcode13.bam sam_to_bam alignments/barcode15.bam sam_to_bam alignments/barcode16.bam sam_to_bam NanoPlot/barcode10/NanoPlot-report.html sample_qa_plot qualimap/barcode10/qualimapReport.html alignment_qa_report NanoPlot/barcode11/NanoPlot-report.html sample_qa_plot NanoPlot/barcode12/NanoPlot-report.html sample_qa_plot NanoPlot/barcode13/NanoPlot-report.html sample_qa_plot NanoPlot/barcode15/NanoPlot-report.html sample_qa_plot NanoPlot/barcode16/NanoPlot-report.html sample_qa_plot references/standardized_genomic.gff standardize_gff NanoPlot/NanoPlot-report.html total_sample_qa_plot merged/all_counts_gene.tsv merged/transcriptid_to_gene_plot.svg transcriptid_to_gene qualimap/barcode11/qualimapReport.html alignment_qa_report qualimap/barcode12/qualimapReport.html alignment_qa_report from workflow configuration 2026-04-07 2026-04-11 Open Science Retreat Global - 2026 Machynlleth, Wales, UK https://digital-research.academy/ https://www.wikidata.org/wiki/Q137737148?wprov=acrw1_0 OpenScience Community members The Snakemake Developer Community is a support group for software packages of the Snakemake Workflow Management System. It organizes events such as hackathons and workshops revolving around a better and reproducible data analysis. Snakemake Community config/config.yaml samples: A: data/samples/A.fastq B: data/samples/B.fastq 2026-03-17T19:26:28.393653+00:00 1 -R '@RG\tID:{sample}\tSM:{sample}' 2 samtools 3 coordinate 4 1 calls/all.vcf calls/positions.png calls/quals.png all all calls/all.vcf envs/bcftools.yml shell bcftools_call sorted_reads/A.bam sorted_reads/B.bam sorted_reads/{sample}.bam envs/bwa.yml v8.1.1/bio/bwa/mem ["-R '@RG\\tID:{sample}\\tSM:{sample}'", "samtools", "coordinate", ""] bwa_mem calls/positions.png envs/matplotlib.yml scripts/plot-positions.py plot_positions calls/quals.png envs/matplotlib.yml scripts/plot-quals.py plot_quals sorted_reads/A.bam.bai sorted_reads/B.bam.bai sorted_reads/{sample}.bam.bai envs/samtools.yml v5.7.0/bio/samtools/index [""] samtools_index from workflow configuration 2026-03-17T16:56:38.233861+00:00 1 -R '@RG\tID:{sample}\tSM:{sample}' 2 samtools 3 coordinate 4 1 all all calls/all.vcf envs/bcftools.yml shell bcftools_call sorted_reads/A.bam sorted_reads/B.bam sorted_reads/{sample}.bam envs/bwa.yml v8.1.1/bio/bwa/mem ["-R '@RG\\tID:{sample}\\tSM:{sample}'", "samtools", "coordinate", ""] bwa_mem calls/positions.png envs/matplotlib.yml scripts/plot-positions.py plot_positions calls/quals.png envs/matplotlib.yml scripts/plot-quals.py plot_quals sorted_reads/A.bam.bai sorted_reads/B.bam.bai sorted_reads/{sample}.bam.bai envs/samtools.yml v5.7.0/bio/samtools/index [""] samtools_index {"samples": {"A": "data/samples/A.fastq", "B": "data/samples/B.fastq"}} config/config.yaml Snakefile config/config.yaml envs/bcftools.yml envs/bwa.yml envs/matplotlib.yml envs/samtools.yml scripts/plot-positions.py scripts/plot-quals.py /home/meesters/Documents/Teaching/snakemake-hpc-teaching-material/snakemake-tutorial/Snakefile /home/meesters/Documents/Teaching/snakemake-hpc-teaching-material/snakemake-tutorial/Snakefile {} 8 2 6 There is already work ongoing for the java library: https://github.com/Nanopublication/nanopub-py/issues/215 , https://github.com/Nanopublication/nanopub-java/compare/master...56-add-sem-release-workflow Could nanopub-py linked with the release-please action (creating automated releases and registering with PyPi in one go)? I would require an organizational GitHub token (from which the java library could profit, too). the snakemake tutorial workflow in various conditions. Snakemake HPC Teaching Material HTML XML PDF workflow report has the description has license has the title is a has primary source workflow data catalog is archived at was published on will be no longer after from has repository results from has source URI of institution/organization where report is archived Template for describing a workflow report Describing a workflow report Report: ${title} Computational Workflow description of the report date when report availability expires (YYYY-MM-DD) license of the published report URI, ROR of insitution/organization where report was produced URI of research project in which report was produced date when made publicly available (YYYY-MM-DD) short URI suffix or full URI URI of repository where report is published title of the report URI of workflow nanopub that is the primary source of this report This is an example report for the Snakemake analysis workflow to analyse differential gene expression and isoform splicing analysis on Nanopore long-read RNA-Seq data using minimap2, Salmon, and DESeq2 : https://github.com/snakemake-workflows/rna-longseq-de-isoform/ Example Snakemake Report 2026-03-04 This nanopub template contains an error, should not be placed under datasets and is currently not retractable. date is a has name is further described by end time located in start time hybrid event in-person event virtual event has event organizer has event sponsor has participating community This template can be used to define a Retreat - describe the purpose, here. Defining a Retreat Events community - a community that has partecipated in the event (starting) date of the event (e.g. 2020-12-31) [0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] short name, used as URI suffix finish date of the event (e.g. 2020-12-31) location of the event (URL or name) the name of the event online resource organizer of the event (ROR, URL or name) sponsor of the event (ROR or name) 0 1 2 3 4 6 7 8 9 10 11 5 Testing data set for a Snakemake differential and splicing isoform detection workflow based on ONT RNA-longseq data FASTA FASTQ fitch program GCG GenBank format genpept GFF2-seq GFF3-seq giFASTA format pdbatom created by has description needs or produces data format has license has title improves upon method CC-BY-4.0 serves purpose applies to domains has source repository has keywords uses computational approach is accessible via Apache 2.0 BSD 3 Clause GPL 3.0 MIT applicable research domains https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= primary computational purpose https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= Template for describing a computational workflow implemented for and supported by a Workflow Management System Computational Workflow Method: ${title} Computational Workflow method this improves upon (DOI or URI) computational approach used https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= URI of the workflow repository ORCID of creator https://orcid.org/ ORCID (just the 16-digit ID) 0000-\d{4}-\d{4}-\d{4} description of what the method does [\s\S]{10,1000} DOI URL https://doi.org/ DOI (starting with '10.') 10.(\d)+/(\S)+ GitHub repository URL expected input data format input: Input: research keywords from Wikidata https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= software license title of the Workflow [\s\S]{5,200} Workflow Management System uses workflow management system Snakemake Workflow Management System Nextflow Galaxy CWL A Snakemake workflow analysing ONT RNA-Seq transcriptomics data to yield differential expression results along with splicing isoforms detection. rna-longseq-de-isoform FASTA FASTQ fitch program GCG GenBank format genpept GFF2-seq GFF3-seq giFASTA format pdbatom created by has description needs or produces data format has license has title improves upon method CC-BY-4.0 serves purpose applies to domains has source repository has keywords uses computational approach reports performance results is accessible via Apache 2.0 BSD 3 Clause GPL 3.0 MIT applicable research domains https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= primary computational purpose https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= Template for describing a computational workflow implemented for and supported by a Workflow Management System Computational Workflow (without target namespace) Method: ${title} Computational Workflow method this improves upon (DOI or URI) computational approach used https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= URI of the workflow repository ORCID of creator https://orcid.org/ ORCID (just the 16-digit ID) 0000-\d{4}-\d{4}-\d{4} description of what the method does [\s\S]{10,1000} DOI URL https://doi.org/ DOI (starting with '10.') 10.(\d)+/(\S)+ GitHub repository URL expected input data format input: Input: research keywords from Wikidata https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search= software license quantitative performance measurements [\s\S]{10,1000} title of the Workflow [\s\S]{5,200} Workflow Management System uses workflow management system Snakemake Workflow Management System Nextflow Galaxy CWL I think we need to have an "onboarding SOP" for - people who start authenticating others for the first time. - for 3rd party lecturers who introduce nanopubs in workshops It could be a slide set or a static part of the homepage or ... anything else without too much effort. What do you think? 2026-03-09 2026-03-13 Snakemake Hackathon Munich, Germany Christian Meesters Clemens Lange David Lähnemann Johannes Köster Lukas Heinrich Matthew Feickert date is a has name is further described by end time located in start time hybrid event in-person event virtual event has event organizer has event sponsor has participating community This template can be used to define a Hackathon Event. Defining a Hackathon Event Events community - a community that has partecipated in the event (starting) date of the event (e.g. 2020-12-31) [0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] short name, used as URI suffix finish date of the event (e.g. 2020-12-31) location of the event (URL or name) the name of the event online resource organizer of the event (ROR, URL or name) sponsor of the event (ROR or name) 0 1 2 3 4 6 7 8 9 10 11 5 Ah, I was thinking, should the "Plan to attend" nanopub template not have a description? A text label, as not all URLs are descriptive? And there it is! The template is updated. Already! How about adding the option to link it with another nanopub? A declared event? And the declared event should have a descriptive field, too. ;-) What do you think? The German Research Software Engineering (deRSE26) takes place from March 3 to March 5, 2026 at the University of Stuttgart. Contributions from all computational fields are welcome. German Research Software Engineering Conference 2026 9. October 2025 An introduction to Continuous Integration Continuous Integration Course Data Analysis Workflow on HPC Systems Snakemake HPC Teaching Material virtual screening results (tabulated enthalpies) Quick, “Imputation-free” meta-analysis with proxy-SNPs