[ { "create_time": "2026-07-08", "creators": [ "Amirhossein Naghsh Nilchi", "Pavankumar Videm" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.2174.5", "edam_operation": [ "Differential gene expression analysis", "Expression profile clustering", "Differential gene expression profiling", "Principal component visualisation" ], "edam_topic": [ "Single-cell sequencing" ], "id": "2174", "keep": true, "latest_version": 5, "license": "MIT", "link": "https://workflowhub.eu/workflows/2174?version=5", "name": "Galaxy EISTA spatialdata + updated squidpy", "number_of_steps": 80, "projects": [ "usegalaxy-eu" ], "source": "WorkflowHub", "tags": [ "bioinformatics", "galaxy", "single cell clustering", "transcriptomics", "single-cell", "spatial transcriptomics" ], "tools": [ "anndata_manipulate", "tp_cut_tool", "pick_value", "tp_awk_tool", "spatialdata_operation", "addValue", "scanpy_inspect", "collection_column_join", "select the resolution\nCut1", "split_file_to_collection", "scanpy_cluster_reduce_dimension", "scanpy_remove_confounders", "table_compute", "squidpy_graph", "datamash_transpose", "scanpy_plot", "tp_sort_header_tool", "compose_text_param", "map_param_value", "param_value_from_file", "scanpy_filter", "celltypist", "tp_find_and_replace", "liana_methods", "anndata_inspect", "scanpy_normalize", "Add_a_column1", "set the value to a text input\nparam_value_from_file", "tp_replace_in_line" ], "update_time": "2026-07-08", "versions": 5 }, { "create_time": "2026-07-07", "creators": [ "Giuseppe Defazio", "Lucille Delisle", "Paul Zierep" ], "deprecated": false, "doi": null, "edam_operation": [ "Data retrieval", "Deposition" ], "edam_topic": [], "id": "2214", "keep": true, "latest_version": 2, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/2214?version=2", "name": "metadata-and-sequences-from-bioproject-ids/main", "number_of_steps": 7, "projects": [ "Intergalactic Workflow Commission (IWC)" ], "source": "WorkflowHub", "tags": [], "tools": [ "", "pysradb_search", "__RELABEL_FROM_FILE__", "tp_awk_tool", "tp_cat", "BioProject IDs will be furnished as parameters to the pysradb tool\nparam_value_from_file", "split_file_to_collection" ], "update_time": "2026-07-07", "versions": 2 }, { "create_time": "2026-06-18", "creators": [ "Tristan Reynolds", "Ammar Aziz" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.2196.1", "edam_operation": [ "Sequencing quality control", "Phylogenetic analysis" ], "edam_topic": [ "Bioinformatics", "Biomedical science", "Genomics", "Virology" ], "id": "2196", "keep": true, "latest_version": 1, "license": "MIT", "link": "https://workflowhub.eu/workflows/2196?version=1", "name": "MPXV (Mpox) Phylogenetic Analysis with Squirrel", "number_of_steps": 3, "projects": [ "Melbourne Bioinformatics", "Galaxy Australia" ], "source": "WorkflowHub", "tags": [ "amplicon", "mpox", "ont", "virus", "mpxv", "phylogeny" ], "tools": [ "squirrel_phylo", "regex1", "squirrel_qc" ], "update_time": "2026-06-25", "versions": 1 }, { "create_time": "2026-06-18", "creators": [ "Tristan Reynolds", "Ammar Aziz" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.2195.1", "edam_operation": [ "Mapping", "Validation", "Sequencing quality control", "Sequence alignment" ], "edam_topic": [ "Bioinformatics", "Biomedical science", "Genomics", "Virology" ], "id": "2195", "keep": true, "latest_version": 1, "license": "MIT", "link": "https://workflowhub.eu/workflows/2195?version=1", "name": "Viral Amplicon Analysis Pipeline for ONT Data", "number_of_steps": 12, "projects": [ "Melbourne Bioinformatics", "Galaxy Australia" ], "source": "WorkflowHub", "tags": [ "amplicon", "mpox", "ont", "virus", "mpxv", "phylogeny" ], "tools": [ "XY_Plot_1", "mosdepth", "tp_cat", "regex1", "fastplong", "bedtools_makewindowsbed", "artic_minion", "multiqc", "__BUILD_LIST__" ], "update_time": "2026-06-25", "versions": 1 }, { "create_time": "2026-06-15", "creators": [], "deprecated": false, "doi": null, "edam_operation": [ "Data handling", "Visualisation", "Image analysis", "Image annotation" ], "edam_topic": [], "id": "2191", "keep": true, "latest_version": 1, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/2191?version=1", "name": "Histological Staining Area Quantification", "number_of_steps": 29, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "gtn", "galaxy", "name:brightfieldmicroscopy", "name:colordeconvolution", "name:histology", "name:histologystaining", "name:immunohistochemistry", "name:massontrichrome" ], "tools": [ "Paste1", "Cut1", "tp_text_file_with_recurring_lines", "tp_cat", "ip_histogram_equalization", "Grep1", "This final output file contains the merged measurement results for all samples, and can be used for further statistical analysis.\ncat1", "collection_element_identifiers", "collapse_dataset", "ip_threshold", "ip_imageinfo", "Combined the Sample ID with the header of the remaining columns.\nPaste1", "ip_color_deconvolution", "ip_split_image", "This step joins a list of sample names with their corresponding quantification results. It pastes both files side by side, ensuring that each sample name is aligned with the correct row of the quantification table.\nPaste1", "Show tail1", "imagej2_analyze_particles_binary", "tp_sed_tool", "Extracting header from source dataset to use in the final tabular file. \nShow beginning1", "Add_a_column1", "ip_2d_feature_extraction", "This step extracts the second image (usually the relevant stain channel) from each sub-collection in a collection of collections. Please verify the selected channel is correct before proceeding. The current index is set to extract dataset 2.\n__EXTRACT_DATASET__", "Extracts a dataset that will be used to obtain the header row for the final concatenated tabular file in a subsequent step.\n__EXTRACT_DATASET__" ], "update_time": "2026-06-15", "versions": 1 }, { "create_time": "2024-11-04", "creators": [ "Diego De Panis" ], "deprecated": false, "doi": null, "edam_operation": [ "Phasing", "Data handling", "Data deposition", "Genome assembly", "De-novo assembly", "Genotyping", "Scaffolding", "k-mer counting", "Data parsing", "Data retrieval", "Sequence alignment analysis", "Sequence assembly validation", "Mapping", "Visualisation", "Pairwise sequence alignment", "Sequence database search", "Sequence trimming" ], "edam_topic": [ "Genomics" ], "id": "1104", "keep": true, "latest_version": 2, "license": "MIT", "link": "https://workflowhub.eu/workflows/1104?version=2", "name": "Galaxy Workflow ERGA-BGE Genome Report ASM analyses (one-asm Long Reads + HiC)", "number_of_steps": 48, "projects": [ "ERGA Assembly" ], "source": "WorkflowHub", "tags": [ "genome assembly", "genomics", "qc" ], "tools": [ "lftp", "hicexplorer_hicplotmatrix", "Cut1", "bg_diamond", "tp_text_file_with_recurring_lines", "pick_value", "__EXTRACT_DATASET__", "cooler_csort_tabix", "collapse_dataset", "__FLATTEN__", "__ZIP_COLLECTION__", "gfastats", "cooler_cload_tabix", "chromap", "minimap2", "genomescope", "merqury", "smudgeplot", "meryl", "busco", "sambamba_merge", "blobtoolkit", "hicexplorer_hicmergematrixbins", "__UNZIP_COLLECTION__", "sambamba_flagstat", "datasets_download_genome", "bedtools_makewindowsbed", "CONVERTER_fasta_to_fai", "fasterq_dump" ], "update_time": "2026-06-15", "versions": 2 }, { "create_time": "2026-05-30", "creators": [ "Delphine Lariviere" ], "deprecated": false, "doi": null, "edam_operation": [ "Read pre-processing", "Data handling", "Genome visualisation", "Pathway visualisation", "Primer removal", "Sequence trimming", "Structure visualisation" ], "edam_topic": [], "id": "2180", "keep": true, "latest_version": 1, "license": "MIT", "link": "https://workflowhub.eu/workflows/2180?version=1", "name": "post-curation-processing/main", "number_of_steps": 37, "projects": [ "Intergalactic Workflow Commission (IWC)" ], "source": "WorkflowHub", "tags": [], "tools": [ "", "add_line_to_file", "tp_sed_tool", "Cut1", "tp_awk_tool", "tp_text_file_with_recurring_lines", "tp_easyjoin_tool", "compose_text_param", "imagemagick_image_montage", "map_param_value", "compress_file", "mashmap", "pick_value", "jbrowse2", "cutadapt", "join1", "gfastats" ], "update_time": "2026-06-11", "versions": 1 }, { "create_time": "2026-06-12", "creators": [ "Diana Chiang Jurado" ], "deprecated": false, "doi": null, "edam_operation": [ "Data handling", "Visualisation", "Image analysis", "Image annotation" ], "edam_topic": [], "id": "2179", "keep": true, "latest_version": 3, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/2179?version=3", "name": "histological-staining-area-quantification/histological-staining-area-quantification", "number_of_steps": 28, "projects": [ "Intergalactic Workflow Commission (IWC)" ], "source": "WorkflowHub", "tags": [], "tools": [ "Paste1", "Cut1", "tp_text_file_with_recurring_lines", "tp_cat", "This final output file contains the merged measurement results for all samples, and can be used for further statistical analysis.\ncat1", "Grep1", "collection_element_identifiers", "collapse_dataset", "ip_threshold", "ip_imageinfo", "Combined the Sample ID with the header of the remaining columns.\nPaste1", "ip_color_deconvolution", "ip_split_image", "This step joins a list of sample names with their corresponding quantification results. It pastes both files side by side, ensuring that each sample name is aligned with the correct row of the quantification table.\nPaste1", "Show tail1", "imagej2_analyze_particles_binary", "tp_sed_tool", "Extracting header from source dataset to use in the final tabular file. \nShow beginning1", "Add_a_column1", "ip_2d_feature_extraction", "This step extracts the second image (usually the relevant stain channel) from each sub-collection in a collection of collections. Please verify the selected channel is correct before proceeding. The current index is set to extract dataset 2.\n__EXTRACT_DATASET__", "Extracts a dataset that will be used to obtain the header row for the final concatenated tabular file in a subsequent step.\n__EXTRACT_DATASET__" ], "update_time": "2026-06-15", "versions": 3 }, { "create_time": "2026-05-18", "creators": [], "deprecated": false, "doi": null, "edam_operation": [ "Visualisation", "Prediction and recognition" ], "edam_topic": [], "id": "1443", "keep": true, "latest_version": 2, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/1443?version=2", "name": "Metaproteomics_GTN", "number_of_steps": 10, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "gtn", "galaxy", "proteomics" ], "tools": [ "search_gui", "query_tabular", "unipept", "peptide_shaker", "sqlite_to_tabular" ], "update_time": "2026-05-18", "versions": 2 }, { "create_time": "2026-05-18", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1873", "keep": true, "latest_version": 2, "license": "MIT", "link": "https://workflowhub.eu/workflows/1873?version=2", "name": "Final - Modeling Breast Cancer Subtypes (flexynesis only)", "number_of_steps": 10, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "flexynesis", "gtn", "galaxy", "machine_learning", "tabpfn" ], "tools": [ "flexynesis_plot", "tp_sort_header_tool", "__EXTRACT_DATASET__", "flexynesis" ], "update_time": "2026-05-18", "versions": 2 }, { "create_time": "2026-05-18", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1633", "keep": true, "latest_version": 2, "license": "MIT", "link": "https://workflowhub.eu/workflows/1633?version=2", "name": "ml_regression (imported from uploaded file)", "number_of_steps": 11, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "gtn", "galaxy", "ml", "regression", "statistics" ], "tools": [ "Remove beginning1", "sklearn_build_pipeline", "plotly_regression_performance_plots", "sklearn_generalized_linear", "sklearn_searchcv", "sklearn_ensemble" ], "update_time": "2026-05-18", "versions": 2 }, { "create_time": "2026-05-11", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1953", "keep": true, "latest_version": 3, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/1953?version=3", "name": "Introduction to DH in Galaxy", "number_of_steps": 13, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "dh", "digitalhumanities", "gtn", "galaxy", "introduction", "textcleaning" ], "tools": [ "Remove beginning1", "wordcloud", "tp_find_and_replace", "tp_grep_tool", "tp_replace_in_line", "diff" ], "update_time": "2026-05-11", "versions": 3 }, { "create_time": "2026-05-11", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "2170", "keep": true, "latest_version": 1, "license": "MIT", "link": "https://workflowhub.eu/workflows/2170?version=1", "name": "Test tuto yolo DeepSeaSpy", "number_of_steps": 1, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "ai", "ecology", "gtn", "galaxy", "marinebiodiversity", "imaging", "yolo" ], "tools": [ "yolo_predict" ], "update_time": "2026-05-11", "versions": 1 }, { "create_time": "2026-05-11", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1623", "keep": true, "latest_version": 3, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/1623?version=3", "name": "Text-Mining Differences in Chinese Newspaper Articles", "number_of_steps": 10, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "chinese-language", "comparison", "diff", "digitalhumanities", "gtn", "galaxy", "humanities", "text", "text_mining" ], "tools": [ "datamash_ops", "tp_sort_header_tool", "This step selects all lines from the diff file that contain the censorship symbol \u00d7.\nGrep1", "Add_a_column1", "wordcloud", "tp_replace_in_line", "diff", "This step selects only column 9, which contains the uncensored characters from text two. The result is only one column with different rows of Chinese characters. \n\nThis step allows scaling words by frequency the word cloud in the next step. meaning characters that appear more often appear bigger, making the results evident at first sight.\nCut1" ], "update_time": "2026-05-11", "versions": 3 }, { "create_time": "2025-08-25", "creators": [ "Daniela Schneider" ], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1884", "keep": true, "latest_version": 1, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/1884?version=1", "name": "Visualise amount of objects in Museum Collection", "number_of_steps": 16, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "4culture", "visualisation", "culturedata", "openrefine", "tabulardata", "textcleaning" ], "tools": [ "datamash_ops", "Remove beginning1", "Cut1", "tp_sort_header_tool", "regexColumn1", "compose_text_param", "tp_head_tool", "param_value_from_file", "wordcloud", "filter_tabular", "barchart_gnuplot", "tp_grep_tool" ], "update_time": "2026-05-13", "versions": 1 }, { "create_time": "2026-04-17", "creators": [ "Luke Silver", "Anna Syme" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.880.2", "edam_operation": [ "Sequence file editing", "Data handling" ], "edam_topic": [], "id": "880", "keep": true, "latest_version": 2, "license": "GPL-3.0", "link": "https://workflowhub.eu/workflows/880?version=2", "name": "Convert formats - TSI", "number_of_steps": 47, "projects": [ "Australian BioCommons", "Galaxy Australia" ], "source": "WorkflowHub", "tags": [ "tsi-annotation" ], "tools": [ "tp_sed_tool", "fasta_compute_length", "Cut1", "Paste1", "tp_awk_tool", "fasta2tab", "tp_sort_header_tool", "seqtk_seq", "tab2fasta", "tp_grep_tool", "tp_replace_in_line", "seqtk_subseq" ], "update_time": "2026-05-13", "versions": 2 }, { "create_time": "2026-05-05", "creators": [ "Luke Silver" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.881.8", "edam_operation": [ "Sequence assembly validation" ], "edam_topic": [], "id": "881", "keep": true, "latest_version": 8, "license": "GPL-3.0", "link": "https://workflowhub.eu/workflows/881?version=8", "name": "Fgenesh annotation -TSI", "number_of_steps": 10, "projects": [ "Australian BioCommons", "Galaxy Australia" ], "source": "WorkflowHub", "tags": [ "tsi-annotation" ], "tools": [ "jcvi_gff_stats", "fgenesh_get_mrnas_gc", "fgenesh_merge", "fgenesh_annotate", "busco", "fgenesh_split", "fgenesh_get_proteins" ], "update_time": "2026-05-13", "versions": 8 }, { "create_time": "2026-05-04", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1964", "keep": true, "latest_version": 2, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/1964?version=2", "name": "Visualise amount of objects in Museum Collection", "number_of_steps": 16, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "4culture", "gtn", "galaxy", "visualisation", "culturedata", "openrefine", "tabulardata", "textcleaning" ], "tools": [ "datamash_ops", "Remove beginning1", "Cut1", "tp_sort_header_tool", "regexColumn1", "compose_text_param", "tp_head_tool", "param_value_from_file", "wordcloud", "filter_tabular", "barchart_gnuplot", "tp_grep_tool" ], "update_time": "2026-05-04", "versions": 2 }, { "create_time": "2026-05-04", "creators": [ "Maia Kelly", "Christopher Ashwood" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.2167.1", "edam_operation": [], "edam_topic": [ "Biochemistry", "Computational chemistry", "Systems biology" ], "id": "2167", "keep": true, "latest_version": 1, "license": "Apache-2.0", "link": "https://workflowhub.eu/workflows/2167?version=1", "name": "GlyCombo Galaxy", "number_of_steps": 0, "projects": [ "Protea Glycosciences Analytical" ], "source": "WorkflowHub", "tags": [ "galaxy", "glycomics" ], "tools": [], "update_time": "2026-05-04", "versions": 1 }, { "create_time": "2026-05-01", "creators": [ "VGP", " Galaxy" ], "deprecated": false, "doi": null, "edam_operation": [ "k-mer counting" ], "edam_topic": [], "id": "632", "keep": true, "latest_version": 15, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/632?version=15", "name": "kmer-profiling-hifi-VGP1/main", "number_of_steps": 18, "projects": [ "Intergalactic Workflow Commission (IWC)" ], "source": "WorkflowHub", "tags": [], "tools": [ "", "meryl_groups_kmers", "rdeval", "compose_text_param", "imagemagick_image_montage", "collection_column_join", "param_value_from_file", "rdeval_report", "genomescope", "meryl_histogram_kmers", "meryl_count_kmers" ], "update_time": "2026-05-13", "versions": 15 }, { "create_time": "2026-04-27", "creators": [], "deprecated": false, "doi": null, "edam_operation": [], "edam_topic": [], "id": "1648", "keep": true, "latest_version": 2, "license": "CC-BY-4.0", "link": "https://workflowhub.eu/workflows/1648?version=2", "name": "Mitogenome-Assembly-VGP0", "number_of_steps": 3, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "gtn", "galaxy", "reviewed", "vgp" ], "tools": [ "mitohifi", "compress_file" ], "update_time": "2026-04-27", "versions": 2 }, { "create_time": "2026-04-27", "creators": [], "deprecated": false, "doi": null, "edam_operation": [ "Conversion", "Peptide database search" ], "edam_topic": [], "id": "1429", "keep": true, "latest_version": 2, "license": "MIT", "link": "https://workflowhub.eu/workflows/1429?version=2", "name": "Proteogenomics 2: Database Search", "number_of_steps": 7, "projects": [ "Galaxy Training Network" ], "source": "WorkflowHub", "tags": [ "gtn", "galaxy", "proteomics" ], "tools": [ "mz_to_sqlite", "ident_params", "search_gui", "query_tabular", "tab2fasta", "peptide_shaker" ], "update_time": "2026-04-27", "versions": 2 }, { "create_time": "2026-04-19", "creators": [ "Anna Syme" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.226.2", "edam_operation": [ "Variant calling", "Base-calling", "Sequence assembly" ], "edam_topic": [ "Sequence assembly" ], "id": "226", "keep": true, "latest_version": 2, "license": "Apache-2.0", "link": "https://workflowhub.eu/workflows/226?version=2", "name": "Assembly polishing", "number_of_steps": 6, "projects": [ "Galaxy Australia", "Australian BioCommons" ], "source": "WorkflowHub", "tags": [ "large-genome-assembly" ], "tools": [ "\n 01041e6e0464607c", "fasta-stats", "medaka_consensus_pipeline", "\n d5a2cb013d9747c0" ], "update_time": "2026-05-13", "versions": 2 }, { "create_time": "2026-04-21", "creators": [ "Kate Farquharson", "Gareth Price", "Simon Tang", "Anna Syme", "Gareth Price", "Anna Syme" ], "deprecated": false, "doi": "10.48546/workflowhub.workflow.403.11", "edam_operation": [ "Phasing", "Visualisation", "Genome assembly", "De-novo assembly", "Scaffolding", "k-mer counting", "Sequence assembly validation" ], "edam_topic": [], "id": 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