├── .claude └── commands │ └── review.md ├── .flake8 ├── .github ├── PULL_REQUEST_TEMPLATE.md ├── copilot-instructions.md └── workflows │ ├── ci.yaml │ ├── comment_on_pr.yml │ ├── enable_ci_workflows.yml │ ├── gh-build-and-test.yml │ ├── gh-page-build.yml │ ├── pr_without_change.yml │ ├── setup.yml │ ├── slash.yaml │ ├── test_workflows.yml │ ├── usegalaxy-star-installation.yml │ └── workflow_test.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── README.md ├── bump_version.py ├── requirements.txt ├── scripts ├── create_mermaid.py ├── usegalaxy_star_upload.py └── workflow_manifest.py ├── static ├── add-creator.gif ├── iwc-import.gif ├── update_workflow.png └── wf-invocations.png ├── website ├── .gitignore ├── .prettierignore ├── .prettierrc ├── README.md ├── astro.config.mjs ├── new-components-test.png ├── package-lock.json ├── package.json ├── playwright.config.js ├── public │ ├── CNAME │ ├── category-descriptions │ │ ├── computational-chemistry.md │ │ ├── data-fetching.md │ │ ├── epigenetics.md │ │ ├── genome-annotation.md │ │ ├── genome-assembly.md │ │ ├── imaging.md │ │ ├── metabarcoding.md │ │ ├── metabolomics.md │ │ ├── metaproteomics.md │ │ ├── microbiome.md │ │ ├── proteomics.md │ │ ├── sars-cov-2.md │ │ ├── single-cell.md │ │ ├── transcriptomics.md │ │ ├── variant-calling.md │ │ ├── vertebrates-genome-project.md │ │ └── virology.md │ ├── favicon.ico │ ├── iwc_logo.png │ ├── iwc_logo_white.png │ ├── run-flow.png │ ├── waveNounProject.svg │ └── workflow_manifest.json ├── src │ ├── components │ │ ├── Author.vue │ │ ├── CodeBlock.vue │ │ ├── CollectionContent.vue │ │ ├── CollectionHero.vue │ │ ├── Filters.vue │ │ ├── GalaxyInstanceSelector.vue │ │ ├── IWCHeader.astro │ │ ├── MarkdownRenderer.vue │ │ ├── PopularWorkflows.vue │ │ ├── TabPanel.vue │ │ ├── WorkflowCard.vue │ │ ├── WorkflowContent.vue │ │ ├── WorkflowGrid.vue │ │ └── ui │ │ │ ├── Badge.vue │ │ │ ├── Button.vue │ │ │ ├── Card.vue │ │ │ ├── CardContent.vue │ │ │ ├── CardHeader.vue │ │ │ ├── Combobox.vue │ │ │ ├── ComboboxAnchor.vue │ │ │ ├── ComboboxContent.vue │ │ │ ├── ComboboxEmpty.vue │ │ │ ├── ComboboxInput.vue │ │ │ ├── ComboboxItem.vue │ │ │ ├── ComboboxTrigger.vue │ │ │ ├── Select.vue │ │ │ ├── SelectContent.vue │ │ │ ├── SelectItem.vue │ │ │ ├── SelectTrigger.vue │ │ │ ├── SelectValue.vue │ │ │ ├── Tabs.vue │ │ │ ├── TabsContent.vue │ │ │ ├── TabsList.vue │ │ │ ├── TabsTrigger.vue │ │ │ ├── badge-variants.ts │ │ │ └── button-variants.ts │ ├── layouts │ │ └── BaseLayout.astro │ ├── lib │ │ └── utils.ts │ ├── models │ │ └── workflow.ts │ ├── pages │ │ ├── about.astro │ │ ├── collection │ │ │ └── [slug].astro │ │ ├── index.astro │ │ └── workflow │ │ │ └── [id].astro │ ├── stores │ │ └── workflowStore.ts │ ├── styles │ │ └── global.css │ └── utils │ │ ├── index.ts │ │ ├── jsonld.ts │ │ └── manifest.ts ├── tailwind.config.ts ├── tests │ ├── analyze-workflow-page.js │ ├── e2e │ │ ├── basic.spec.js │ │ ├── filter-scroll.spec.js │ │ ├── galaxy-instance-selector.spec.js │ │ └── jsonld.spec.js │ └── test-new-components.js ├── tsconfig.json └── workflow-page-analysis.png └── workflows ├── .flake8 ├── README.md ├── VGP-assembly-v2 ├── Assembly-Hifi-HiC-phasing-VGP4 │ ├── .dockstore.yml │ ├── Assembly-Hifi-HiC-phasing-VGP4-tests.yml │ ├── Assembly-Hifi-HiC-phasing-VGP4.ga │ ├── CHANGELOG.md │ ├── README.md │ └── test-data │ │ └── Genomescope Model Parameters.tabular ├── Assembly-Hifi-Trio-phasing-VGP5 │ ├── .dockstore.yml │ ├── Assembly-Hifi-Trio-phasing-VGP5-tests.yml │ ├── Assembly-Hifi-Trio-phasing-VGP5.ga │ ├── CHANGELOG.md │ ├── README.md │ └── test-data │ │ └── GenomeScope_Model_parameters.tabular ├── Assembly-Hifi-only-VGP3 │ ├── .dockstore.yml │ ├── Assembly-Hifi-only-VGP3-tests.yml │ ├── Assembly-Hifi-only-VGP3.ga │ ├── CHANGELOG.md │ ├── README.md │ └── test-data │ │ └── GenomeScope_Model_parameters.tabular ├── Assembly-decontamination-VGP9 │ ├── .dockstore.yml │ ├── Assembly-decontamination-VGP9-tests.yml │ ├── Assembly-decontamination-VGP9.ga │ ├── CHANGELOG.md │ └── README.md ├── Mitogenome-assembly-VGP0 │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Mitogenome-Assembly-VGP0-tests.yml │ ├── Mitogenome-Assembly-VGP0.ga │ └── README.md ├── Plot-Nx-Size │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Generate-Nx-and-Size-plots-for-multiple-assemblies-tests.yml │ ├── Generate-Nx-and-Size-plots-for-multiple-assemblies.ga │ ├── README.md │ └── test-data │ │ ├── alternate_head.tabular │ │ └── primary_head.tabular ├── Purge-duplicate-contigs-VGP6 │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Purge-duplicate-contigs-VGP6-tests.yml │ ├── Purge-duplicate-contigs-VGP6.ga │ └── README.md ├── Purge-duplicates-one-haplotype-VGP6b │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Purging-duplicates-one-haplotype-VGP6b-tests.yml │ ├── Purging-duplicates-one-haplotype-VGP6b.ga │ └── README.md ├── README.md ├── Scaffolding-Bionano-VGP7 │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── Scaffolding-BioNano-VGP7-tests.yml │ └── Scaffolding-BioNano-VGP7.ga ├── Scaffolding-HiC-VGP8 │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── Scaffolding-HiC-VGP8-tests.yml │ └── Scaffolding-HiC-VGP8.ga ├── hi-c-contact-map-for-assembly-manual-curation │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── hi-c-map-for-assembly-manual-curation-tests.yml │ └── hi-c-map-for-assembly-manual-curation.ga ├── kmer-profiling-hifi-VGP1 │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── kmer-profiling-hifi-VGP1-tests.yml │ ├── kmer-profiling-hifi-VGP1.ga │ └── test-data │ │ ├── GenomeScope_Linear_plot.png │ │ ├── GenomeScope_Log_plot.png │ │ ├── GenomeScope_Transformed_linear_plot.png │ │ └── GenomeScope_Transformed_log_plot.png └── kmer-profiling-hifi-trio-VGP2 │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── kmer-profiling-hifi-trio-VGP2-tests.yml │ ├── kmer-profiling-hifi-trio-VGP2.ga │ └── test-data │ ├── GenomeScope_Linear_plot_child.png │ ├── GenomeScope_Linear_plot_maternal.png │ ├── GenomeScope_Linear_plot_paternal.png │ ├── GenomeScope_Log_plot_child.png │ ├── GenomeScope_Log_plot_maternal.png │ ├── GenomeScope_Log_plot_paternal.png │ ├── GenomeScope_Transformed_linear_plot_child.png │ ├── GenomeScope_Transformed_linear_plot_maternal.png │ ├── GenomeScope_Transformed_linear_plot_paternal.png │ ├── GenomeScope_Transformed_log_plot_child.png │ ├── GenomeScope_Transformed_log_plot_maternal.png │ └── GenomeScope_Transformed_log_plot_paternal.png ├── amplicon ├── amplicon-mgnify │ ├── README.md │ ├── mapseq-to-ampvis2 │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mapseq-to-ampvis2-tests.yml │ │ └── mapseq-to-ampvis2.ga │ ├── mgnify-amplicon-pipeline-v5-complete │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mgnify-amplicon-pipeline-v5-complete-tests.yml │ │ └── mgnify-amplicon-pipeline-v5-complete.ga │ ├── mgnify-amplicon-pipeline-v5-its │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mgnify-amplicon-pipeline-v5-its-tests.yml │ │ └── mgnify-amplicon-pipeline-v5-its.ga │ ├── mgnify-amplicon-pipeline-v5-quality-control-paired-end │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mgnify-amplicon-pipeline-v5-quality-control-paired-end-tests.yml │ │ └── mgnify-amplicon-pipeline-v5-quality-control-paired-end.ga │ ├── mgnify-amplicon-pipeline-v5-quality-control-single-end │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mgnify-amplicon-pipeline-v5-quality-control-single-end-tests.yml │ │ └── mgnify-amplicon-pipeline-v5-quality-control-single-end.ga │ ├── mgnify-amplicon-pipeline-v5-rrna-prediction │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mgnify-amplicon-pipeline-v5-rrna-prediction-tests.yml │ │ └── mgnify-amplicon-pipeline-v5-rrna-prediction.ga │ ├── mgnify-amplicon-taxonomic-summary-tables │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── mgnify-amplicon-summary-tables-tests.yml │ │ └── mgnify-amplicon-summary-tables.ga │ └── taxonomic-rank-abundance-summary-table │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── taxonomic-rank-abundance-summary-table-tests.yml │ │ └── taxonomic-rank-abundance-summary-table.ga ├── dada2 │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── dada2_paired-tests.yml │ ├── dada2_paired.ga │ └── test-data │ │ ├── Counts.tabular │ │ └── Sequence Table.dada2_sequencetable └── qiime2 │ ├── README.md │ ├── qiime2-I-import │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── QIIME2-Ia-multiplexed-data-single-end-tests.yml │ ├── QIIME2-Ia-multiplexed-data-single-end.ga │ ├── QIIME2-Ib-multiplexed-data-paired-end-tests.yml │ ├── QIIME2-Ib-multiplexed-data-paired-end.ga │ ├── QIIME2-Ic-demultiplexed-data-single-end-tests.yml │ ├── QIIME2-Ic-demultiplexed-data-single-end.ga │ ├── QIIME2-Id-demultiplexed-data-paired-end-tests.yml │ ├── QIIME2-Id-demultiplexed-data-paired-end.ga │ └── README.md │ ├── qiime2-II-denoising │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── QIIME2-IIa-denoising-and-feature-table-creation-single-end-tests.yml │ ├── QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga │ ├── QIIME2-IIb-denoising-and-feature-table-creation-paired-end-tests.yml │ ├── QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga │ └── README.md │ └── qiime2-III-VI-downsteam │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml │ ├── QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga │ ├── QIIME2-VI-diversity-metrics-and-estimations-tests.yml │ ├── QIIME2-VI-diversity-metrics-and-estimations.ga │ └── README.md ├── bacterial_genomics ├── amr_gene_detection │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── amr_gene_detection-tests.yml │ └── amr_gene_detection.ga ├── bacterial-quality-and-contamination-control-post-assembly │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── bacterial_quality_and_contamination_control_post_assembly-tests.yml │ └── bacterial_quality_and_contamination_control_post_assembly.ga └── bacterial_genome_annotation │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── bacterial_genome_annotation-tests.yml │ └── bacterial_genome_annotation.ga ├── computational-chemistry ├── fragment-based-docking-scoring │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── fragment-based-docking-scoring-tests.yml │ ├── fragment-based-docking-scoring.ga │ └── test-data │ │ ├── all-fragments.sdf │ │ ├── candidates.smi │ │ ├── receptor.pdb │ │ └── single-fragment.sdf ├── gromacs-dctmd │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── gromacs-dctmd-tests.yml │ ├── gromacs-dctmd.ga │ ├── test-data │ │ ├── lig.sdf │ │ └── mpro.pdb │ └── tmd.mdp ├── gromacs-mmgbsa │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── gromacs-mmgbsa-tests.yml │ ├── gromacs-mmgbsa.ga │ └── test-data │ │ ├── lig.sdf │ │ └── mpro.pdb └── protein-ligand-complex-parameterization │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── protein-ligand-complex-parameterization-tests.yml │ ├── protein-ligand-complex-parameterization.ga │ └── test-data │ ├── complex.gro │ ├── complex.top │ ├── lig.sdf │ └── mpro.pdb ├── data-fetching ├── parallel-accession-download │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── parallel-accession-download-tests.yml │ ├── parallel-accession-download.ga │ └── test-data │ │ ├── SRR044777_head.fastq │ │ ├── SRR11953971_1_head.fastq │ │ ├── SRR11953971_2_head.fastq │ │ ├── input_accession_paired_end.txt │ │ └── input_accession_single_end.txt └── sra-manifest-to-concatenated-fastqs │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── sra-manifest-to-concatenated-fastqs-tests.yml │ ├── sra-manifest-to-concatenated-fastqs.ga │ └── test-data │ └── SRA.txt ├── enable_ci_workflows.py ├── epigenetics ├── atacseq │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── atacseq-tests.yml │ └── atacseq.ga ├── average-bigwig-between-replicates │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── average-bigwig-between-replicates-tests.yml │ └── average-bigwig-between-replicates.ga ├── chipseq-pe │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── chipseq-pe-tests.yml │ └── chipseq-pe.ga ├── chipseq-sr │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── chipseq-sr-tests.yml │ └── chipseq-sr.ga ├── consensus-peaks │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── consensus-peaks-atac-cutandrun-tests.yml │ ├── consensus-peaks-atac-cutandrun.ga │ ├── consensus-peaks-chip-pe-tests.yml │ ├── consensus-peaks-chip-pe.ga │ ├── consensus-peaks-chip-sr-tests.yml │ ├── consensus-peaks-chip-sr.ga │ ├── generate_fake_reads.R │ ├── strategy.png │ └── test-data │ │ ├── ChIP_SR_rep1.bam │ │ ├── ChIP_SR_rep2.bam │ │ ├── ChIP_SR_rep3.bam │ │ ├── rep1.bam │ │ ├── rep2.bam │ │ └── rep3.bam ├── cutandrun │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── cutandrun-tests.yml │ ├── cutandrun.ga │ └── test-data │ │ ├── SRR15904259_subset_forward.fastqsanger.gz │ │ └── SRR15904259_subset_reverse.fastqsanger.gz └── hic-hicup-cooler │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── chic-fastq-to-cool-hicup-cooler-tests.yml │ ├── chic-fastq-to-cool-hicup-cooler.ga │ ├── hic-fastq-to-cool-hicup-cooler-tests.yml │ ├── hic-fastq-to-cool-hicup-cooler.ga │ ├── hic-fastq-to-pairs-hicup-tests.yml │ ├── hic-fastq-to-pairs-hicup.ga │ ├── hic-juicermediumtabix-to-cool-cooler-tests.yml │ ├── hic-juicermediumtabix-to-cool-cooler.ga │ └── test-data │ ├── plot_chic.png │ ├── plot_hic.png │ └── valid_pairs_filtered_and_sorted.juicer_medium_tabix.gz ├── gen_crates.py ├── genome-assembly ├── assembly-with-flye │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Genome-assembly-with-Flye-tests.yml │ ├── Genome-assembly-with-Flye.ga │ ├── README.md │ └── test-data │ │ └── Input_reads.fastqsanger.gz ├── bacterial-genome-assembly │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── bacterial_genome_assembly-tests.yml │ └── bacterial_genome_assembly.ga ├── polish-with-long-reads │ ├── .dockstore.yml │ ├── Assembly-polishing-with-long-reads-tests.yml │ ├── Assembly-polishing-with-long-reads.ga │ ├── CHANGELOG.md │ ├── README.md │ └── test-data │ │ ├── assembly.fasta │ │ ├── assembly_polished_by_long_reads.fasta │ │ └── long_reads.fastqsanger.gz └── quality-and-contamination-control-raw-reads │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── quality_and_contamination_control_raw_reads-tests.yml │ └── quality_and_contamination_control_raw_reads.ga ├── genome_annotation ├── annotation-braker3 │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Genome_annotation_with_braker3-tests.yml │ ├── Genome_annotation_with_braker3.ga │ └── README.md ├── annotation-helixer │ ├── CHANGELOG.md │ ├── Galaxy-Workflow-annotation_helixer-tests.yml │ ├── Galaxy-Workflow-annotation_helixer.ga │ └── README.md ├── annotation-maker │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Genome_annotation_with_maker_short.ga │ ├── Genome_annotation_with_maker_short_tests.yml │ └── README.md ├── functional-annotation │ └── functional-annotation-protein-sequences │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── Functional_annotation_of_protein_sequences-tests.yml │ │ ├── Functional_annotation_of_protein_sequences.ga │ │ └── README.md └── lncRNAs-annotation │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Galaxy-Workflow-lncRNAs_annotation_workflow-tests.yml │ ├── Galaxy-Workflow-lncRNAs_annotation_workflow.ga │ └── README.md ├── imaging ├── fluorescence-nuclei-segmentation-and-counting │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── segmentation-and-counting-tests.yml │ ├── segmentation-and-counting.ga │ └── test-data │ │ ├── input_image.tiff │ │ ├── label_image.tiff │ │ ├── objects_count.tabular │ │ └── overlay_image.png └── tissue-microarray-analysis │ ├── multiplex-tissue-microarray-analysis │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── multiplex-tma-tests.yml │ ├── multiplex-tma.ga │ └── test-data │ │ ├── Manual Gates.csv │ │ ├── Markers File.csv │ │ └── Phenotype workflow.csv │ └── tissue-microarray-analysis │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── test-data │ ├── markers.csv │ └── phenotypes.csv │ ├── tissue-micro-array-analysis-tests.yml │ └── tissue-micro-array-analysis.ga ├── metabolomics ├── gcms-metams │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Mass-spectrometry__GCMS-with-metaMS-tests.yml │ ├── Mass-spectrometry__GCMS-with-metaMS.ga │ ├── README.md │ └── test-data │ │ └── metaMS.runGC_dataMatrix.tabular ├── lcms-preprocessing │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml │ ├── Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga │ ├── README.md │ └── test-data │ │ ├── xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv │ │ └── xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv ├── mfassignr │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── mfassignr-tests.yml │ ├── mfassignr.ga │ └── test-data │ │ ├── Ambig.tabular │ │ ├── None.tabular │ │ ├── Unambig.tabular │ │ ├── final_series.tabular │ │ └── recal_series.tabular └── qcxms-sdf │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── QCxMS-Spectra-Prediction-from-SDF-tests.yml │ ├── QCxMS-Spectra-Prediction-from-SDF.ga │ ├── README.md │ └── test-data │ └── Input SDF File.sdf ├── microbiome ├── host-contamination-removal │ ├── host-contamination-removal-long-reads │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── host-or-contamination-removal-on-long-reads-tests.yml │ │ └── host-or-contamination-removal-on-long-reads.ga │ └── host-contamination-removal-short-reads │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── host-or-contamination-removal-on-short-reads-tests.yml │ │ └── host-or-contamination-removal-on-short-reads.ga ├── mags-building │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── MAGs-generation-tests.yml │ ├── MAGs-generation.ga │ └── README.md ├── metagenomic-genes-catalogue │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── metagenomic-genes-catalogue-tests.yml │ └── metagenomic-genes-catalogue.ga └── pathogen-identification │ ├── README.md │ ├── allele-based-pathogen-identification │ ├── .dockstore.yml │ ├── Allele-based-Pathogen-Identification-tests.yml │ ├── Allele-based-Pathogen-Identification.ga │ ├── CHANGELOG.md │ ├── README.md │ └── test-data │ │ └── mapping_mean_depth_per_sample.tabular │ ├── gene-based-pathogen-identification │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Gene-based-Pathogen-Identification-tests.yml │ ├── Gene-based-Pathogen-Identification.ga │ ├── README.md │ └── test-data │ │ └── extracted_samples_IDs.txt │ ├── nanopore-pre-processing │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Nanopore-Pre-Processing-tests.yml │ ├── Nanopore-Pre-Processing.ga │ ├── README.md │ └── test-data │ │ └── nanoplot_qc_on_reads_after_preprocessing_nanostats_collection_of_all_samples_Spike3bBarcode12.tabular │ ├── pathogen-detection-pathogfair-samples-aggregation-and-visualisation │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation-tests.yml │ ├── Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga │ ├── README.md │ └── test-data │ │ ├── adjusted_abricate_vfs_tabular_part1_YP_001006764.tabular │ │ ├── amr_identified_by_ncbi_collection_of_all_samples_Spike3bBarcode10.fastq.gz.tabular │ │ ├── amr_identified_by_ncbi_collection_of_all_samples_Spike3bBarcode12.fastq.gz.tabular │ │ ├── amrs_split_file_000000.txt.tabular │ │ ├── amrs_split_file_000001.txt.tabular │ │ ├── contigs_split_file_000000.txt.fasta │ │ ├── contigs_split_file_000001.txt.fasta │ │ ├── mapping_coverage_percentage_per_sample.tabular │ │ ├── mapping_mean_depth_per_sample.tabular │ │ ├── number_of_variants_per_sample.tabular │ │ ├── removed_hosts_percentage_tabular.tabular │ │ ├── vfs_of_genes_identified_by_vfdb_collection_of_all_samples_Spike3bBarcode10.fastq.gz.tabular │ │ ├── vfs_of_genes_identified_by_vfdb_collection_of_all_samples_Spike3bBarcode12.fastq.gz.tabular │ │ ├── vfs_split_file_000000.txt.tabular │ │ └── vfs_split_file_000001.txt.tabular │ └── taxonomy-profiling-and-visualization-with-krona │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── Taxonomy-Profiling-and-Visualization-with-Krona-tests.yml │ ├── Taxonomy-Profiling-and-Visualization-with-Krona.ga │ └── test-data │ └── converted_kraken_report_collection_of_all_samples_Spike3bBarcode12.tabular ├── proteomics ├── clinicalmp │ ├── clinicalmp-data-interpretation │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── WF5_Data_Interpretation_Worklow.ga │ │ ├── WF5_Data_Interpretation_Worklow_tests.yml │ │ └── test-data │ │ │ ├── Annotation.tabular │ │ │ ├── Comparison_Matrix.tabular │ │ │ ├── Human_Proteins.tabular │ │ │ ├── MaxQuant_Evidence.tabular │ │ │ ├── MaxQuant_Protein_Groups.tabular │ │ │ ├── Microbial_Proteins.tabular │ │ │ └── Quantified_Peptides.tabular │ ├── clinicalmp-database-generation │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── iwc-clinicalmp-database-generation-tests.yml │ │ └── iwc-clinicalmp-database-generation.ga │ ├── clinicalmp-discovery │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── iwc-clinicalmp-discovery-workflow-tests.yml │ │ ├── iwc-clinicalmp-discovery-workflow.ga │ │ └── test-data │ │ │ └── Experimental Design Discovery MaxQuant.tabular │ ├── clinicalmp-quantitation │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── iwc-clinicalmp-quantitation-tests.yml │ │ ├── iwc-clinicalmp-quantitation.ga │ │ └── test-data │ │ │ ├── Quantified-Peptides.tabular │ │ │ └── Quantified-Proteins.tabular │ └── clinicalmp-verification │ │ ├── .dockstore.yml │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── clinicalmp-verification-tests.yml │ │ ├── clinicalmp-verification.ga │ │ └── test-data │ │ ├── Distinct_Peptides_for_PepQuery.tabular │ │ ├── MaxQuant-peptide-report.tabular │ │ ├── Peptide_and_Protein_from_Peptide_Reports.tabular │ │ ├── SGPS_peptide-report.tabular │ │ ├── Uniprot-ID_from_verified_Peptides.tabular │ │ └── cRAP.fasta └── openms-metaprosip │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── metaprosip-tests.yml │ └── metaprosip.ga ├── read-preprocessing └── short-read-qc-trimming │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── short-read-quality-control-and-trimming-tests.yml │ └── short-read-quality-control-and-trimming.ga ├── repeatmasking ├── .dockstore.yml ├── .workflowhub.yml ├── CHANGELOG.md ├── README.md ├── Repeat-masking-with-RepeatModeler-and-RepeatMasker-tests.yml ├── RepeatMasking-Workflow-tests.yml └── RepeatMasking-Workflow.ga ├── requirements.txt ├── sars-cov-2-variant-calling ├── sars-cov-2-consensus-from-variation │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── consensus-from-variation-tests.yml │ ├── consensus-from-variation.ga │ └── test-data │ │ ├── aligned_reads_for_coverage.bam │ │ ├── final_snpeff_annotated_variants.vcf │ │ └── masked_consensus.fa ├── sars-cov-2-ont-artic-variant-calling │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── ont-artic-variation-tests.yml │ ├── ont-artic-variation.ga │ └── test-data │ │ └── final_snpeff_annotated_variants.vcf ├── sars-cov-2-pe-illumina-artic-ivar-analysis │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── pe-wgs-ivar-analysis-test.yml │ └── pe-wgs-ivar-analysis.ga ├── sars-cov-2-pe-illumina-artic-variant-calling │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── pe-artic-variation-tests.yml │ └── pe-artic-variation.ga ├── sars-cov-2-pe-illumina-wgs-variant-calling │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── pe-wgs-variation-tests.yml │ ├── pe-wgs-variation.ga │ └── test-data │ │ └── final_snpeff_annotated_variants.vcf ├── sars-cov-2-se-illumina-wgs-variant-calling │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── se-wgs-variation-tests.yml │ └── se-wgs-variation.ga └── sars-cov-2-variation-reporting │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── test-data │ ├── by_variant_report.tsv │ ├── combined_variant_report.tsv │ ├── ont-artic.vcf │ ├── pe-artic.vcf │ ├── pe-illumina-wgs.vcf │ └── se-illumina-wgs.vcf │ ├── variation-reporting-tests.yml │ └── variation-reporting.ga ├── scRNAseq ├── baredsc │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── baredSC-1d-logNorm-tests.yml │ ├── baredSC-1d-logNorm.ga │ ├── baredSC-2d-logNorm-tests.yml │ ├── baredSC-2d-logNorm.ga │ └── test-data │ │ ├── combined_1d_plot.png │ │ ├── combined_2d_plot.png │ │ └── nih3t3_generated_2d_2.txt ├── fastq-to-matrix-10x │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml │ ├── scrna-seq-fastq-to-matrix-10x-cellplex.ga │ ├── scrna-seq-fastq-to-matrix-10x-v3-tests.yml │ ├── scrna-seq-fastq-to-matrix-10x-v3.ga │ └── test-data │ │ └── all_cell_barcodes_both_versions.txt ├── pseudobulk-worflow-decoupler-edger │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── pseudo-bulk_edgeR-tests.yml │ └── pseudo-bulk_edgeR.ga ├── scanpy-clustering │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── Preprocessing-and-Clustering-of-single-cell-RNA-seq-data-with-Scanpy-tests.yml │ ├── Preprocessing-and-Clustering-of-single-cell-RNA-seq-data-with-Scanpy.ga │ ├── README.md │ └── test-data │ │ ├── General information about the final Anndata object.txt │ │ └── final_anndata_general_info.txt └── velocyto │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── Velocyto-on10X-filtered-barcodes-tests.yml │ ├── Velocyto-on10X-filtered-barcodes.ga │ ├── Velocyto-on10X-from-bundled-tests.yml │ └── Velocyto-on10X-from-bundled.ga ├── transcriptomics ├── brew3r │ ├── .dockstore.yml │ ├── BREW3R-tests.yml │ ├── BREW3R.ga │ ├── CHANGELOG.md │ ├── README.md │ └── test-data │ │ ├── GSM4196550_subset.bam │ │ ├── GSM4196551_subset.bam │ │ ├── GSM4196552_subset.bam │ │ └── input.gtf ├── goseq │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── goseq-go-kegg-enrichment-analsis-tests.yml │ └── goseq-go-kegg-enrichment-analsis.ga ├── rnaseq-de │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── rnaseq-de-filtering-plotting-tests.yml │ └── rnaseq-de-filtering-plotting.ga ├── rnaseq-pe │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── rnaseq-pe-tests.yml │ └── rnaseq-pe.ga └── rnaseq-sr │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── rnaseq-sr-tests.yml │ └── rnaseq-sr.ga ├── variant-calling ├── generic-variant-calling-wgs-pe │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── Generic-variation-analysis-on-WGS-PE-data-tests.yml │ ├── Generic-variation-analysis-on-WGS-PE-data.ga │ ├── README.md │ └── test-data │ │ ├── ERR3485802.forward.fastq.gz │ │ ├── ERR3485802.reverse.fastq.gz │ │ ├── Fasta sequences for genbank file.fasta │ │ ├── GenBank genome.genbank │ │ ├── SnpEff variants.vcf │ │ ├── called_variants.vcf │ │ ├── mapped_reads_stats.tabular │ │ └── soft_filtered_variants.vcf ├── haploid-variant-calling-wgs-pe │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── WGS-PE-variant-calling-in-haploid-system-tests.yml │ ├── WGS-PE-variant-calling-in-haploid-system.ga │ └── test-data │ │ └── Annotated Variants.tabular └── variation-reporting │ ├── .dockstore.yml │ ├── .workflowhub.yml │ ├── CHANGELOG.md │ ├── Generic-variation-analysis-reporting-tests.yml │ ├── Generic-variation-analysis-reporting.ga │ ├── README.md │ └── test-data │ ├── Variation data to report_filtered variants ERR3485802.vcf │ ├── af_recalculated.tabular │ ├── all_variants_all_samples.tabular │ ├── by_variant_report.tabular │ └── combined_variant_report.tabular ├── virology ├── generic-non-segmented-viral-variant-calling │ ├── .dockstore.yml │ ├── CHANGELOG.md │ ├── README.md │ ├── pe-illumina-simple-virus-calling-and-consensus-test.yml │ ├── pe-illumina-simple-virus-calling-and-consensus.ga │ └── test-data │ │ ├── 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