diff --git a/communities/microgalaxy/metadata/workflow_status.tsv b/communities/microgalaxy/metadata/workflow_status.tsv index 5be5194b..8807333c 100644 --- a/communities/microgalaxy/metadata/workflow_status.tsv +++ b/communities/microgalaxy/metadata/workflow_status.tsv @@ -1,9 +1,21 @@ Link Name Source Projects Creators Creation time Update time To keep Deprecated +https://workflowhub.eu/workflows/1225?version=1 clinicalmp-discovery/main WorkflowHub Intergalactic Workflow Commission (IWC) Subina Mehta 2024-12-10 2025-01-13 True False +https://workflowhub.eu/workflows/1219?version=1 clinicalmp-data-interpretation/main WorkflowHub Intergalactic Workflow Commission (IWC) GalaxyP 2024-11-26 2024-12-06 True False +https://workflowhub.eu/workflows/1218?version=1 clinicalmp-verification/main WorkflowHub Intergalactic Workflow Commission (IWC) Pratik Jagtap 2024-11-26 2024-12-06 True False +https://workflowhub.eu/workflows/1216?version=1 clinicalmp-database-generation/main WorkflowHub Intergalactic Workflow Commission (IWC) Subina Mehta 2024-11-23 2024-12-06 True False +https://workflowhub.eu/workflows/1177?version=1 clinicalmp-quantitation/main WorkflowHub Intergalactic Workflow Commission (IWC) GalaxyP 2024-10-07 2024-10-07 True False https://workflowhub.eu/workflows/1043?version=7 bacterial-genome-assembly/main WorkflowHub Intergalactic Workflow Commission (IWC) Abromics None, Pierre Marin, Clea Siguret 2024-11-26 2024-11-26 True False https://workflowhub.eu/workflows/1052?version=8 quality-and-contamination-control/main WorkflowHub Intergalactic Workflow Commission (IWC) ABRomics None, Pierre Marin, Clea Siguret 2024-11-23 2024-11-23 True False +https://workflowhub.eu/workflows/1090?version=2 qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub Intergalactic Workflow Commission (IWC) Debjyoti Ghosh 2024-11-26 2024-12-06 True False +https://workflowhub.eu/workflows/1063?version=3 allele-based-pathogen-identification/main WorkflowHub Intergalactic Workflow Commission (IWC) Engy Nasr, Bérénice Batut, Paul Zierep 2024-10-30 2024-10-31 True False +https://workflowhub.eu/workflows/1062?version=1 gene-based-pathogen-identification/main WorkflowHub Intergalactic Workflow Commission (IWC) Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 True False +https://workflowhub.eu/workflows/1060?version=1 pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub Intergalactic Workflow Commission (IWC) Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 True False +https://workflowhub.eu/workflows/1059?version=1 taxonomy-profiling-and-visualization-with-krona/main WorkflowHub Intergalactic Workflow Commission (IWC) Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 True False https://workflowhub.eu/workflows/1050?version=9 bacterial_genome_annotation/main WorkflowHub Intergalactic Workflow Commission (IWC) ABRomics None, Pierre Marin, Clea Siguret 2024-10-26 2024-10-26 True False https://workflowhub.eu/workflows/1049?version=7 amr_gene_detection/main WorkflowHub Intergalactic Workflow Commission (IWC) ABRomics None, Pierre Marin, Clea Siguret 2024-10-26 2024-10-27 True False +https://workflowhub.eu/workflows/790?version=2 dada2/main WorkflowHub Intergalactic Workflow Commission (IWC) Matthias Bernt 2024-05-30 2024-06-02 True False https://workflowhub.eu/workflows/439?version=2 pox-virus-amplicon/main WorkflowHub Intergalactic Workflow Commission (IWC) Viktoria Isabel Schwarz, Wolfgang Maier 2024-06-22 2024-06-22 True False +https://workflowhub.eu/workflows/749?version=1 Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub EuroScienceGateway Anthony Bretaudeau 2024-02-14 2024-02-15 True False https://workflowhub.eu/workflows/406?version=1 GTN Training - Antibiotic Resistance Detection WorkflowHub Galaxy Training Network Saskia Hiltemann, Willem de Koning 2022-11-24 2023-02-13 True False https://workflowhub.eu/workflows/103?version=1 3: Plant virus exploration WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2023-02-13 True False https://workflowhub.eu/workflows/102?version=1 2: Plant virus confirmation WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2023-02-13 True False @@ -17,10 +29,17 @@ https://workflowhub.eu/workflows/651?version=1 Workflow 5: OTU Clustering [16S M https://workflowhub.eu/workflows/650?version=1 Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False https://workflowhub.eu/workflows/648?version=1 Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False https://workflowhub.eu/workflows/649?version=1 Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/1035?version=1 TB Variant Analysis v1.0 WorkflowHub SANBI Pathogen Bioinformatics Peter van Heusden 2024-06-07 2024-06-12 True False +https://workflowhub.eu/workflows/407?version=1 Workflow 3: AMR - SeqSero2/SISTR WorkflowHub Seq4AMR 2022-11-24 2024-09-09 True False +https://workflowhub.eu/workflows/644?version=1 Workflow 2: Sciensano WorkflowHub Seq4AMR 2023-11-07 2024-09-09 True False https://workflowhub.eu/workflows/470?version=1 Workflow 4: Staramr WorkflowHub Seq4AMR 2023-05-11 2024-09-09 True False +https://workflowhub.eu/workflows/634?version=1 Workflow 1: AbritAMR WorkflowHub Seq4AMR 2023-10-31 2024-09-09 True False https://workflowhub.eu/workflows/1189?version=2 AMR-Pathfinder WorkflowHub Seq4AMR, ErasmusMC Clinical Bioinformatics Helena Rasche, Dennis Dollée, Birgit Rijvers 2024-11-14 2024-12-24 True False https://dev.workflowhub.eu/workflows/1380?version=1 Query a metaplasmidome database to identify and annotate plasmids in metagenomes dev.WorkflowHub Galaxy Training Network 2025-01-13 2025-01-20 True False https://dev.workflowhub.eu/workflows/1366?version=1 Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' dev.WorkflowHub Galaxy Training Network 2024-10-07 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1349?version=1 Calculating diversity from microbiome taxonomic data dev.WorkflowHub Galaxy Training Network 2024-08-12 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1344?version=1 Quality and contamination control in bacterial isolate using Illumina MiSeq Data dev.WorkflowHub Galaxy Training Network 2024-07-15 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1217?version=2 Checking expected species and contamination in bacterial isolate dev.WorkflowHub Galaxy Training Network 2024-07-16 2024-10-07 True False https://dev.workflowhub.eu/workflows/1133?version=1 Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1129?version=1 Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1125?version=1 Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False @@ -33,7 +52,9 @@ https://dev.workflowhub.eu/workflows/1101?version=1 Training: 16S rRNA Sequencin https://dev.workflowhub.eu/workflows/1097?version=1 Identification of the micro-organisms in a beer using Nanopore sequencing dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1095?version=1 Taxonomic Profiling and Visualization of Metagenomic Data dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1080?version=1 Workflow 3: Functional Information (quick) dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1078?version=1 pox-virus-tiled-amplicon-ref-masking dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1070?version=1 Amplicon Tutorial dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1069?version=2 TB Variant Analysis v1.0 dev.WorkflowHub Galaxy Training Network 2024-07-16 2024-10-07 True False https://dev.workflowhub.eu/workflows/1067?version=1 "WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1064?version=1 Training: 16S rRNA Analysis with Nanopore Sequencing Reads dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False https://dev.workflowhub.eu/workflows/1060?version=1 Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False diff --git a/communities/microgalaxy/metadata/workflow_tags b/communities/microgalaxy/metadata/workflow_tags index 37153bfa..50a225e8 100644 --- a/communities/microgalaxy/metadata/workflow_tags +++ b/communities/microgalaxy/metadata/workflow_tags @@ -15,4 +15,14 @@ workflowhub: - metatranscriptomics - microbiome - pathogfair -- virology \ No newline at end of file +- virology +- antimicrobial resistance +- pathogen +- name:amplicon +- clinicalmp +- Sciensano +- AbritAMR +- Taxonomic +- taxonomy-profiling +- prokaryote +- tuberculosis \ No newline at end of file diff --git a/communities/microgalaxy/resources/curated_workflows.json b/communities/microgalaxy/resources/curated_workflows.json new file mode 100644 index 00000000..c22116c3 --- /dev/null +++ b/communities/microgalaxy/resources/curated_workflows.json @@ -0,0 +1,3305 @@ +[ + { + "create_time": "2024-12-10", + "creators": [ + "Valentine Murigneux", + "Mike Thang" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.1199.2", + "edam_operation": [ + "Visualisation", + "Taxonomic classification", + "Aggregation", + "Statistical calculation" + ], + "edam_topic": [ + "Metagenomics", + "Taxonomy" + ], + "id": "1199", + "keep": true, + "latest_version": 2, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1199?version=2", + "name": "Taxonomy classification using Kraken2 and Bracken", + "number_of_steps": 29, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "gucfg2galaxy", + "metagenomics", + "name:collection", + "shotgun" + ], + "tools": [ + "__RELABEL_FROM_FILE__", + "krakentools_alpha_diversity", + "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1", + "kraken2", + "add_line_to_file", + "Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1", + "cat_multiple", + "collection_column_join", + "krakentools_combine_kreports", + "taxonomy_krona_chart", + "regex1", + "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", + "Prepare alpha diversity summary file\nPaste1", + "collection_element_identifiers", + "est_abundance", + "krakentools_beta_diversity", + "Extract column name and fraction_total_reads from Bracken report\nCut1", + "krakentools_kreport2krona" + ], + "update_time": "2024-12-10", + "versions": 2 + }, + { + "create_time": "2024-11-14", + "creators": [ + "Helena Rasche", + "Dennis Doll\u00e9e", + "Birgit Rijvers" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Antimicrobial resistance prediction", + "Data handling", + "Genome assembly", + "Parsing" + ], + "edam_topic": [], + "id": "1189", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/1189?version=2", + "name": "AMR-Pathfinder", + "number_of_steps": 36, + "projects": [ + "Seq4AMR", + "ErasmusMC Clinical Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "amr", + "amr-detection", + "benchamrking" + ], + "tools": [ + "", + "cat1", + "__APPLY_RULES__", + "Cut1", + "tp_text_file_with_recurring_lines", + "datamash_ops", + "collapse_dataset", + "Grep1", + "tp_find_and_replace", + "addValue", + "__MERGE_COLLECTION__", + "staramr_search", + "tp_split_on_column", + "shovill", + "hamronize_summarize", + "cat_multi_datasets", + "abricate", + "cast", + "hamronize_tool" + ], + "update_time": "2024-12-24", + "versions": 2 + }, + { + "create_time": "2024-11-26", + "creators": [ + "Abromics None", + "Pierre Marin", + "Clea Siguret" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence assembly visualisation", + "Data handling", + "Genome assembly", + "Parsing", + "Sequence assembly validation", + "Visualisation" + ], + "edam_topic": [], + "id": "1043", + "keep": true, + "latest_version": 7, + "license": "GPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1043?version=7", + "name": "bacterial-genome-assembly/main", + "number_of_steps": 7, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "abromics", + "assembly", + "fastq", + "genomics", + "bacterial-genomics", + "paired-end", + "quality" + ], + "tools": [ + "tooldistillator", + "bandage_info", + "tooldistillator_summarize", + "shovill", + "quast", + "refseq_masher_matches", + "bandage_image" + ], + "update_time": "2024-11-26", + "versions": 7 + }, + { + "create_time": "2024-11-23", + "creators": [ + "ABRomics None", + "Pierre Marin", + "Clea Siguret" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Data handling", + "Statistical calculation", + "Sequence contamination filtering", + "Taxonomic classification", + "Parsing", + "Cross-assembly", + "Expression analysis", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "1052", + "keep": true, + "latest_version": 8, + "license": "GPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1052?version=8", + "name": "quality-and-contamination-control/main", + "number_of_steps": 6, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "abromics", + "fastq", + "genomics", + "bacterial-genomics", + "paired-end", + "quality", + "taxonomy-assignment", + "trimming" + ], + "tools": [ + "recentrifuge", + "tooldistillator", + "tooldistillator_summarize", + "kraken2", + "fastp", + "est_abundance" + ], + "update_time": "2024-11-23", + "versions": 8 + }, + { + "create_time": "2023-05-11", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Antimicrobial resistance prediction", + "Data handling", + "Genome assembly", + "Parsing" + ], + "edam_topic": [], + "id": "470", + "keep": true, + "latest_version": 1, + "license": "GPL-3.0", + "link": "https://workflowhub.eu/workflows/470?version=1", + "name": "Workflow 4: Staramr", + "number_of_steps": 10, + "projects": [ + "Seq4AMR" + ], + "source": "WorkflowHub", + "tags": [ + "10.3390/microorganisms10020292", + "amr", + "amr-detection", + "bioinformatics", + "antimicrobial resistance" + ], + "tools": [ + "abricate", + "tp_find_and_replace", + "shovill", + "hamronize_tool", + "hamronize_summarize", + "collapse_dataset", + "staramr_search" + ], + "update_time": "2024-09-09", + "versions": 1 + }, + { + "create_time": "2024-10-26", + "creators": [ + "ABRomics None", + "Pierre Marin", + "Clea Siguret" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Structural variation detection", + "Nucleic acid feature detection", + "Protein feature detection", + "Genome assembly", + "Parsing", + "Sequence motif recognition", + "Genome annotation", + "Data handling", + "Multilocus sequence typing", + "Scaffolding" + ], + "edam_topic": [], + "id": "1050", + "keep": true, + "latest_version": 9, + "license": "GPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1050?version=9", + "name": "bacterial_genome_annotation/main", + "number_of_steps": 6, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "abromics", + "annotation", + "genomics", + "bacterial-genomics", + "fasta", + "genome-annotation" + ], + "tools": [ + "tooldistillator", + "tooldistillator_summarize", + "integron_finder", + "isescan", + "plasmidfinder", + "bakta" + ], + "update_time": "2024-10-26", + "versions": 9 + }, + { + "create_time": "2024-10-26", + "creators": [ + "ABRomics None", + "Pierre Marin", + "Clea Siguret" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Antimicrobial resistance prediction", + "Data handling", + "Parsing" + ], + "edam_topic": [], + "id": "1049", + "keep": true, + "latest_version": 7, + "license": "GPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1049?version=7", + "name": "amr_gene_detection/main", + "number_of_steps": 5, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "abromics", + "amr", + "amr-detection", + "genomics", + "antibiotic-resistance", + "antimicrobial resistance", + "antimicrobial-resistance-genes", + "bacterial-genomics", + "fasta" + ], + "tools": [ + "abricate", + "tooldistillator", + "tooldistillator_summarize", + "amrfinderplus", + "staramr_search" + ], + "update_time": "2024-10-27", + "versions": 7 + }, + { + "create_time": "2023-10-26", + "creators": [ + "Valentine Murigneux", + "Mike Thang", + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.624.1", + "edam_operation": [ + "Visualisation", + "Phylogenetic tree analysis", + "Nucleic acid sequence analysis" + ], + "edam_topic": [ + "Metagenomic sequencing", + "Metagenomics" + ], + "id": "624", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/624?version=1", + "name": "Analyses of shotgun metagenomics data with MetaPhlAn2", + "number_of_steps": 17, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "gucfg2galaxy", + "metagenomics", + "shotgun" + ], + "tools": [ + "", + "metaphlan2", + "humann2", + "merge_metaphlan_tables", + "Cut1", + "taxonomy_krona_chart", + "humann2_renorm_table", + "humann2_regroup_table", + "metaphlan2krona" + ], + "update_time": "2024-04-05", + "versions": 1 + }, + { + "create_time": "2023-11-09", + "creators": [ + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut", + "Dave Clements", + "Ahmed Mehdi" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Phylogenetic tree analysis", + "Phylogenetic tree generation", + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Phylogenetic tree reconstruction", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "653", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/653?version=1", + "name": "Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]", + "number_of_steps": 4, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "mothur_heatmap_sim", + "newick_display", + "mothur_dist_shared", + "mothur_tree_shared" + ], + "update_time": "2023-11-09", + "versions": 1 + }, + { + "create_time": "2023-11-09", + "creators": [ + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut", + "Dave Clements", + "Ahmed Mehdi" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "652", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/652?version=1", + "name": "Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]", + "number_of_steps": 3, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "mothur_rarefaction_single", + "mothur_summary_single", + "XY_Plot_1" + ], + "update_time": "2023-11-09", + "versions": 1 + }, + { + "create_time": "2023-11-09", + "creators": [ + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut", + "Dave Clements", + "Ahmed Mehdi" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "651", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/651?version=1", + "name": "Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]", + "number_of_steps": 5, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "mothur_classify_otu", + "mothur_sub_sample", + "mothur_count_groups", + "mothur_make_shared", + "mothur_cluster_split" + ], + "update_time": "2023-11-09", + "versions": 1 + }, + { + "create_time": "2023-11-09", + "creators": [ + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut", + "Dave Clements", + "Ahmed Mehdi" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "650", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/650?version=1", + "name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 2, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "mothur_classify_seqs", + "mothur_remove_lineage" + ], + "update_time": "2023-11-09", + "versions": 1 + }, + { + "create_time": "2023-11-09", + "creators": [ + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut", + "Dave Clements", + "Ahmed Mehdi" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "648", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/648?version=1", + "name": "Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]", + "number_of_steps": 5, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "mothur_summary_seqs", + "mothur_screen_seqs", + "mothur_unique_seqs", + "mothur_count_seqs" + ], + "update_time": "2023-11-09", + "versions": 1 + }, + { + "create_time": "2023-11-09", + "creators": [ + "Saskia Hiltemann", + "B\u00e9r\u00e9nice Batut", + "Dave Clements", + "Ahmed Mehdi" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "649", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/649?version=1", + "name": "Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur]", + "number_of_steps": 9, + "projects": [ + "QCIF Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "mothur_screen_seqs", + "mothur_unique_seqs", + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_summary_seqs", + "mothur_chimera_vsearch", + "mothur_pre_cluster" + ], + "update_time": "2023-11-09", + "versions": 1 + }, + { + "create_time": "2024-06-22", + "creators": [ + "Viktoria Isabel Schwarz", + "Wolfgang Maier" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence analysis", + "Sequence alignment analysis", + "Generation", + "Sequence alignment", + "Sequencing quality control", + "Read mapping", + "Validation", + "Local alignment", + "Sequence contamination filtering", + "Genome indexing", + "Global alignment" + ], + "edam_topic": [], + "id": "439", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/439?version=2", + "name": "pox-virus-amplicon/main", + "number_of_steps": 40, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "virology", + "pox" + ], + "tools": [ + "\n __FLATTEN__", + "\n __ZIP_COLLECTION__", + "datamash_ops", + "tp_cat", + "compose_text_param", + "\n __SORTLIST__", + "qualimap_bamqc", + "fasta_compute_length", + "\n Cut1", + "ivar_consensus", + "\n param_value_from_file", + "samtools_view", + "\n __APPLY_RULES__", + "EMBOSS: maskseq51", + "multiqc", + "ivar_trim", + "fastp", + "split_file_to_collection", + "samtools_stats", + "\n Grep1", + "samtools_merge", + "tp_sed_tool", + "collection_element_identifiers", + "\n __FILTER_FAILED_DATASETS__", + "bwa_mem" + ], + "update_time": "2024-06-22", + "versions": 2 + }, + { + "create_time": "2021-02-04", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence contamination filtering", + "Genome assembly", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "103", + "keep": true, + "latest_version": 1, + "license": "Apache-2.0", + "link": "https://workflowhub.eu/workflows/103?version=1", + "name": "3: Plant virus exploration", + "number_of_steps": 2, + "projects": [ + "Integrated and Urban Plant Pathology Laboratory" + ], + "source": "WorkflowHub", + "tags": [ + "de_novo", + "virology", + "exploration" + ], + "tools": [ + "fastp", + "shovill" + ], + "update_time": "2023-02-13", + "versions": 1 + }, + { + "create_time": "2021-02-04", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Variant calling", + "Pairwise sequence alignment", + "Sequence contamination filtering", + "Read pre-processing", + "Genome assembly", + "Formatting", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "102", + "keep": true, + "latest_version": 1, + "license": "Apache-2.0", + "link": "https://workflowhub.eu/workflows/102?version=1", + "name": "2: Plant virus confirmation", + "number_of_steps": 7, + "projects": [ + "Integrated and Urban Plant Pathology Laboratory" + ], + "source": "WorkflowHub", + "tags": [ + "assembly", + "virology", + "blast", + "mapping", + "reads_selection" + ], + "tools": [ + "ncbi_blastn_wrapper", + "shovill", + "minimap2", + "ngsutils_bam_filter", + "samtools_stats", + "fasta_merge_files_and_filter_unique_sequences", + "picard_SamToFastq" + ], + "update_time": "2023-02-13", + "versions": 1 + }, + { + "create_time": "2022-11-24", + "creators": [ + "Saskia Hiltemann", + "Willem de Koning" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence analysis", + "Scatter plot plotting", + "Pairwise sequence alignment", + "Sequence assembly visualisation", + "Genome assembly", + "Aggregation", + "De-novo assembly", + "Box-Whisker plot plotting", + "Mapping assembly" + ], + "edam_topic": [ + "Microbiology" + ], + "id": "406", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/406?version=1", + "name": "GTN Training - Antibiotic Resistance Detection", + "number_of_steps": 12, + "projects": [ + "Galaxy Training Network" + ], + "source": "WorkflowHub", + "tags": [ + "metagenomics" + ], + "tools": [ + "PlasFlow", + "miniasm", + "unicycler", + "gfa_to_fa", + "minimap2", + "racon", + "nanoplot", + "bandage_image", + "staramr_search" + ], + "update_time": "2023-02-13", + "versions": 1 + }, + { + "create_time": "2021-06-17", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Taxonomic classification" + ], + "edam_topic": [], + "id": "124", + "keep": true, + "latest_version": 1, + "license": "Apache-2.0", + "link": "https://workflowhub.eu/workflows/124?version=1", + "name": "1: Plant virus detection with kraken2 (SE)", + "number_of_steps": 3, + "projects": [ + "Integrated and Urban Plant Pathology Laboratory" + ], + "source": "WorkflowHub", + "tags": [ + "virology", + "kraken" + ], + "tools": [ + "kraken2", + "taxonomy_krona_chart", + "Kraken2Tax" + ], + "update_time": "2023-02-13", + "versions": 1 + }, + { + "create_time": "2021-02-04", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Taxonomic classification" + ], + "edam_topic": [], + "id": "101", + "keep": true, + "latest_version": 1, + "license": "Apache-2.0", + "link": "https://workflowhub.eu/workflows/101?version=1", + "name": "1: Plant virus detection with kraken2 (PE)", + "number_of_steps": 3, + "projects": [ + "Integrated and Urban Plant Pathology Laboratory" + ], + "source": "WorkflowHub", + "tags": [ + "virology", + "kraken" + ], + "tools": [ + "kraken2", + "taxonomy_krona_chart", + "Kraken2Tax" + ], + "update_time": "2023-02-13", + "versions": 1 + }, + { + "create_time": "2025-01-13", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Pairwise sequence alignment" + ], + "edam_topic": [], + "id": "1380", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1380?version=1", + "name": "Query a metaplasmidome database to identify and annotate plasmids in metagenomes", + "number_of_steps": 47, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "metaplasmidome", + "name:microgalaxy", + "metagenomics" + ], + "tools": [ + "MQoutputfilter", + "join1", + "tp_replace_in_column", + "ggplot2_histogram", + "cat1", + "sort1", + "tp_sorted_uniq", + "CONVERTER_fasta_to_tabular", + "minimap2", + "count_gff_features", + "Filter1", + "tab2fasta", + "Cut1", + "Add_a_column1", + "tp_tail_tool", + "add_column_headers", + "Grouping1", + "histogram_rpy" + ], + "update_time": "2025-01-20", + "versions": 1 + }, + { + "create_time": "2024-10-07", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence feature detection", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1366", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1366?version=1", + "name": "Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'", + "number_of_steps": 1, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "fungi", + "gtn", + "galaxy", + "lotus2", + "ecology", + "metagenomics" + ], + "tools": [ + "lotus2" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1133", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1133?version=1", + "name": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 6, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_classify_otu", + "mothur_remove_groups", + "mothur_sub_sample", + "mothur_count_groups", + "mothur_make_shared", + "mothur_cluster_split" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1129", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1129?version=1", + "name": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 3, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_rarefaction_single", + "mothur_summary_single", + "XY_Plot_1" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1125", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1125?version=1", + "name": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 4, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_dist_seqs", + "mothur_rarefaction_single", + "mothur_make_shared", + "mothur_cluster" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1121", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1121?version=1", + "name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 5, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_summary_seqs", + "mothur_screen_seqs", + "mothur_unique_seqs", + "mothur_count_seqs" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Phylogenetic tree analysis", + "Phylogenetic tree generation", + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Phylogenetic tree reconstruction", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1117", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1117?version=1", + "name": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 6, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_heatmap_sim", + "mothur_venn", + "mothur_dist_shared", + "mothur_tree_shared", + "newick_display", + "collapse_dataset" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1112", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1112?version=1", + "name": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 9, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_screen_seqs", + "mothur_unique_seqs", + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_summary_seqs", + "mothur_chimera_vsearch", + "mothur_pre_cluster" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence analysis", + "Scatter plot plotting", + "Pairwise sequence alignment", + "Sequence assembly visualisation", + "Genome assembly", + "Aggregation", + "De-novo assembly", + "Box-Whisker plot plotting", + "Mapping assembly" + ], + "edam_topic": [], + "id": "1107", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://dev.workflowhub.eu/workflows/1107?version=1", + "name": "Copy Of GTN Training - Antibiotic Resistance Detection", + "number_of_steps": 12, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "PlasFlow", + "miniasm", + "unicycler", + "gfa_to_fa", + "minimap2", + "racon", + "nanoplot", + "bandage_image", + "staramr_search" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-07-16", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Deposition", + "Variant calling", + "Analysis", + "Visualisation", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1105", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1105?version=2", + "name": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", + "number_of_steps": 21, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "tp_head_tool", + "dada2_plotQualityProfile", + "tp_replace_in_column", + "dada2_filterAndTrim", + "cat1", + "dada2_mergePairs", + "dada2_seqCounts", + "phyloseq_from_dada2", + "dada2_learnErrors", + "dada2_dada", + "collection_element_identifiers", + "dada2_removeBimeraDenovo", + "__UNZIP_COLLECTION__", + "tp_replace_in_line", + "dada2_assignTaxonomyAddspecies", + "__SORTLIST__", + "Add_a_column1", + "dada2_makeSequenceTable" + ], + "update_time": "2024-10-07", + "versions": 2 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Phylogenetic tree analysis", + "Phylogenetic tree generation", + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Phylogenetic tree reconstruction", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1101", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://dev.workflowhub.eu/workflows/1101?version=1", + "name": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial", + "number_of_steps": 38, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_heatmap_sim", + "XY_Plot_1", + "mothur_dist_shared", + "mothur_count_seqs", + "mothur_cluster", + "mothur_make_shared", + "mothur_tree_shared", + "mothur_align_seqs", + "mothur_unique_seqs", + "mothur_taxonomy_to_krona", + "mothur_get_groups", + "mothur_sub_sample", + "mothur_remove_lineage", + "mothur_rarefaction_single", + "mothur_seq_error", + "mothur_pre_cluster", + "mothur_screen_seqs", + "mothur_make_contigs", + "mothur_remove_groups", + "mothur_remove_seqs", + "newick_display", + "taxonomy_krona_chart", + "mothur_summary_seqs", + "mothur_classify_seqs", + "mothur_summary_single", + "mothur_classify_otu", + "mothur_filter_seqs", + "mothur_dist_seqs", + "mothur_venn", + "mothur_make_biom", + "mothur_count_groups", + "mothur_cluster_split", + "mothur_chimera_vsearch" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence composition calculation", + "Visualisation", + "Sequence contamination filtering", + "Taxonomic classification", + "Aggregation", + "Statistical calculation", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "1097", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1097?version=1", + "name": "Identification of the micro-organisms in a beer using Nanopore sequencing", + "number_of_steps": 8, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "porechop", + "kraken2", + "Filter1", + "fastqc", + "fastp", + "taxonomy_krona_chart", + "krakentools_kreport2krona" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Phylogenetic tree analysis", + "Nucleic acid sequence analysis", + "Visualisation", + "Taxonomic classification", + "Aggregation", + "Statistical calculation" + ], + "edam_topic": [], + "id": "1095", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1095?version=1", + "name": "Taxonomic Profiling and Visualization of Metagenomic Data", + "number_of_steps": 10, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "metaphlan", + "kraken2", + "interactive_tool_pavian", + "interactive_tool_phinch", + "est_abundance", + "__UNZIP_COLLECTION__", + "kraken_biom", + "taxonomy_krona_chart", + "krakentools_kreport2krona" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Species frequency estimation", + "Taxonomic classification", + "Phylogenetic analysis" + ], + "edam_topic": [], + "id": "1080", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1080?version=1", + "name": "Workflow 3: Functional Information (quick)", + "number_of_steps": 12, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "asaim", + "metagenomics" + ], + "tools": [ + "humann_regroup_table", + "Grep1", + "humann_split_stratified_table", + "tp_find_and_replace", + "combine_metaphlan2_humann2", + "Cut1", + "humann_unpack_pathways", + "humann_rename_table", + "humann_renorm_table" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1070", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://dev.workflowhub.eu/workflows/1070?version=1", + "name": "Amplicon Tutorial", + "number_of_steps": 17, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "krona-text", + "mothur_screen_seqs", + "mothur_unique_seqs", + "mothur_classify_otu", + "mothur_filter_seqs", + "mothur_cluster_split", + "mothur_merge_files", + "mothur_make_biom", + "mothur_count_seqs", + "mothur_make_shared", + "mothur_make_group", + "mothur_summary_seqs", + "mothur_classify_seqs", + "mothur_align_seqs", + "mothur_pre_cluster" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation" + ], + "edam_topic": [], + "id": "1067", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://dev.workflowhub.eu/workflows/1067?version=1", + "name": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"", + "number_of_steps": 7, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "metaphlan2", + "humann2", + "taxonomy_krona_chart", + "humann2_renorm_table", + "humann2_regroup_table", + "metaphlan2krona" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence composition calculation", + "Validation", + "Visualisation", + "Sequence contamination filtering", + "Taxonomic classification", + "Statistical calculation", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "1064", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://dev.workflowhub.eu/workflows/1064?version=1", + "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads", + "number_of_steps": 11, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "datamash_reverse", + "porechop", + "Remove beginning1", + "kraken2", + "multiqc", + "fastqc", + "fastp", + "tp_replace_in_line", + "taxonomy_krona_chart" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Phylogenetic analysis", + "Sequence clustering", + "Sequence read processing", + "Sequencing quality control", + "Taxonomic classification", + "DNA barcoding" + ], + "edam_topic": [], + "id": "1060", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1060?version=1", + "name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]", + "number_of_steps": 3, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "microbiome" + ], + "tools": [ + "mothur_summary_seqs", + "mothur_classify_seqs", + "mothur_remove_lineage" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-05-06", + "creators": [ + " EMBL's European Bioinformatics Institute", + "Rand Zoabi", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "02f90a96d01fed4f", + "keep": true, + "latest_version": 151, + "license": "Apache-2.0", + "link": "https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f", + "name": "MGnify's amplicon pipeline v5.0", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "metagenomics", + "amplicon", + "name:microgalaxy" + ], + "tools": [ + "CONVERTER_uncompressed_to_gz", + "CONVERTER_gz_to_uncompressed", + "tp_awk_tool", + "__MERGE_COLLECTION__", + "fastq_dl" + ], + "update_time": "2025-01-27", + "versions": 151 + }, + { + "create_time": "2024-03-25", + "creators": [ + "MGnify - EMBL", + "Rand Zoabi", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Validation", + "Read pre-processing", + "Sequence contamination filtering", + "Statistical calculation", + "Sequence trimming", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "b7166aff73e5d81c", + "keep": true, + "latest_version": 20, + "license": "Apache-2.0", + "link": "https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c", + "name": "MGnify's amplicon pipeline v5.0 - Quality control SE", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "amplicon", + "metagenomics", + "name:microgalaxy" + ], + "tools": [ + "trimmomatic", + "tp_find_and_replace", + "fastq_filter", + "multiqc", + "fastqc", + "cshl_fasta_formatter", + "fastq_to_fasta_python", + "prinseq" + ], + "update_time": "2025-01-27", + "versions": 20 + }, + { + "create_time": "2024-05-27", + "creators": [ + "EMBL's European Bioinformatics Institute", + "Rand Zoabi", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Read pre-processing", + "Nucleic acid design", + "Sequencing quality control", + "Sequence trimming", + "Validation", + "Sequence contamination filtering", + "Statistical calculation" + ], + "edam_topic": [], + "id": "f9648091c06171cd", + "keep": true, + "latest_version": 20, + "license": "Apache-2.0", + "link": "https://usegalaxy.eu/published/workflow?id=f9648091c06171cd", + "name": "MGnify's amplicon pipeline v5.0 - Quality control PE", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "amplicon", + "metagenomics", + "name:microgalaxy" + ], + "tools": [ + "trimmomatic", + "tp_find_and_replace", + "fastq_filter", + "mgnify_seqprep", + "fastqc", + "cshl_fasta_formatter", + "fastp", + "multiqc", + "fastq_to_fasta_python", + "__UNZIP_COLLECTION__", + "prinseq" + ], + "update_time": "2025-01-27", + "versions": 20 + }, + { + "create_time": "2024-09-27", + "creators": [ + "Rand Zoabi" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "b57fa7ac24a1e777", + "keep": true, + "latest_version": 4, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=b57fa7ac24a1e777", + "name": "Taxonomic abundance summary tables for a specified taxonomic rank", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "amplicon", + "metagenomics", + "name:microgalaxy" + ], + "tools": [ + "map_param_value", + "collection_column_join", + "Grouping1", + "tp_awk_tool", + "filter_tabular" + ], + "update_time": "2025-01-20", + "versions": 4 + }, + { + "create_time": "2024-05-06", + "creators": [ + "EMBL's European Bioinformatics Institute", + "Rand Zoabi", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Comparison", + "Nucleic acid feature detection", + "Formatting", + "k-mer counting", + "Visualisation", + "Alignment", + "Mapping" + ], + "edam_topic": [], + "id": "0c3eee883f5ab977", + "keep": true, + "latest_version": 38, + "license": "Apache-2.0", + "link": "https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977", + "name": "MGnify's amplicon pipeline v5.0 - rRNA prediction", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "metagenomics", + "amplicon", + "name:microgalaxy" + ], + "tools": [ + "cmsearch_deoverlap", + "__FILTER_EMPTY_DATASETS__", + "gops_concat_1", + "__FILTER_FROM_FILE__", + "infernal_cmsearch", + "bedtools_getfastabed", + "cshl_fasta_formatter", + "query_tabular", + "collection_element_identifiers", + "mapseq", + "biom_convert", + "taxonomy_krona_chart", + "tp_awk_tool" + ], + "update_time": "2025-01-20", + "versions": 38 + }, + { + "create_time": "2024-05-06", + "creators": [ + "EMBL's European Bioinformatics Institute", + "Rand Zoabi", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Visualisation", + "Mapping", + "Formatting", + "k-mer counting" + ], + "edam_topic": [], + "id": "169327ba670607d1", + "keep": true, + "latest_version": 28, + "license": "Apache-2.0", + "link": "https://usegalaxy.eu/published/workflow?id=169327ba670607d1", + "name": "MGnify's amplicon pipeline v5.0 - ITS", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "amplicon", + "metagenomics", + "name:microgalaxy" + ], + "tools": [ + "__FILTER_EMPTY_DATASETS__", + "__FILTER_FROM_FILE__", + "collection_element_identifiers", + "mapseq", + "biom_convert", + "taxonomy_krona_chart", + "bedtools_maskfastabed", + "tp_awk_tool" + ], + "update_time": "2025-01-20", + "versions": 28 + }, + { + "create_time": "2024-05-22", + "creators": [ + "Rand Zoabi" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "05dc8f4321a42cdc", + "keep": true, + "latest_version": 75, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=05dc8f4321a42cdc", + "name": "MGnify amplicon summary tables", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "mgnify_amplicon", + "amplicon", + "metagenomics", + "name:microgalaxy" + ], + "tools": [ + "collection_column_join", + "query_tabular", + "Grouping1", + "tp_awk_tool", + "filter_tabular" + ], + "update_time": "2025-01-14", + "versions": 75 + }, + { + "create_time": "2024-09-30", + "creators": [ + "Valerie C. Schiml", + "Magnus \u00d8. Arntzen", + "B\u00e9r\u00e9nice Batut" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence analysis", + "Sequence generation", + "Protein feature detection", + "Read pre-processing", + "Visualisation", + "Format validation", + "Sequence trimming", + "Local alignment", + "Coding region prediction", + "Conversion", + "Sequence profile generation", + "Taxonomic classification", + "Gene functional annotation", + "Formatting", + "Sequence assembly", + "Sequence composition calculation", + "Probabilistic sequence generation", + "Gene prediction", + "Sequence database search", + "Sequence assembly validation", + "Sequencing quality control", + "Data retrieval", + "Sequence motif recognition", + "Primer removal", + "Validation", + "Multiple sequence alignment", + "Statistical calculation", + "Database search" + ], + "edam_topic": [], + "id": "667bac8d7453e5f1", + "keep": true, + "latest_version": 14, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1", + "name": "MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes ", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:microbiome", + "name:mags" + ], + "tools": [ + "coverm_genome", + "tp_cat", + "coverm_contig", + "cat_bins", + "kofamscan", + "maxbin2", + "sort1", + "trim_galore", + "quast", + "fastqc", + "fraggenescan", + "fasplit", + "checkm_lineage_wf", + "tp_grep_tool", + "hmmer_hmmscan", + "tp_awk_tool", + "interproscan" + ], + "update_time": "2024-12-21", + "versions": 14 + }, + { + "create_time": "2024-12-20", + "creators": [ + "B\u00e9r\u00e9nice Batut", + "G\u00e9raldine Piot" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Phylogenetic tree analysis", + "Species frequency estimation", + "Visualisation", + "Aggregation", + "Phylogenetic analysis", + "Read mapping", + "Standardisation and normalisation", + "Sequencing quality control", + "Nucleic acid sequence analysis", + "Conversion", + "Sequence contamination filtering", + "Taxonomic classification", + "Statistical calculation", + "Formatting" + ], + "edam_topic": [], + "id": "cb2df493f5e334f7", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7", + "name": "Metagenomic Taxonomy and Functional Analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:metagenomics", + "microbiome", + "diversity", + "name:microgalaxy" + ], + "tools": [ + "csv_to_tabular", + "metaphlan", + "cat1", + "bowtie2", + "__UNZIP_COLLECTION__", + "datamash_transpose", + "tp_text_file_with_recurring_lines", + "humann_renorm_table", + "collapse_dataset", + "add_line_to_file", + "sort1", + "Remove beginning1", + "tp_replace_in_line", + "taxpasta", + "humann_unpack_pathways", + "humann_rename_table", + "humann_regroup_table", + "krakentools_alpha_diversity", + "kraken2", + "humann", + "fastp", + "est_abundance", + "fastq_paired_end_interlacer", + "taxonomy_krona_chart", + "tp_easyjoin_tool", + "tp_awk_tool", + "__ZIP_COLLECTION__", + "tp_sed_tool", + "collection_column_join", + "collection_element_identifiers", + "krakentools_kreport2krona" + ], + "update_time": "2024-12-20", + "versions": 2 + }, + { + "create_time": "2024-12-20", + "creators": [ + "Subina Mehta", + "Marie Crane", + "Emma Leith", + "B\u00e9r\u00e9nice Batut", + "Saskia Hiltemann", + "Magnus \u00d8 Arntzen", + "Benoit J. Kunath", + "Phillip B. Pope", + "Francesco Delogu", + "Ray Sajulga", + "Praveen Kumar", + "James E. Johnson", + "Timothy J. Griffin", + "Pratik D. Jagtap" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Sequence alignment analysis", + "Read pre-processing", + "Visualisation", + "Sequence comparison", + "Phylogenetic tree visualisation", + "Sequence trimming", + "Sequencing quality control", + "Phylogenetic tree editing", + "Validation", + "Conversion", + "Phylogenetic inference", + "Primer removal", + "Sequence similarity search", + "Taxonomic classification", + "Statistical calculation", + "Formatting" + ], + "edam_topic": [], + "id": "096b75501c8e0888", + "keep": true, + "latest_version": 3, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=096b75501c8e0888", + "name": "ASaiM-MT: Metatranscriptomics Analysis of Microbes", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "asaim", + "metatranscriptomics", + "rna-seq", + "microbiome", + "name:microgalaxy" + ], + "tools": [ + "combine_metaphlan2_humann2", + "format_metaphlan2_output", + "humann2_genefamilies_genus_level", + "metaphlan2", + "Grep1", + "humann2_unpack_pathways", + "export2graphlan", + "Grouping1", + "graphlan", + "humann2_renorm_table", + "metaphlan2krona", + "multiqc", + "fastqc", + "group_humann2_uniref_abundances_to_go", + "fastq_paired_end_interlacer", + "taxonomy_krona_chart", + "graphlan_annotate", + "cutadapt", + "humann2", + "bg_sortmerna", + "tp_sort_header_tool" + ], + "update_time": "2024-12-20", + "versions": 3 + }, + { + "create_time": "2024-12-20", + "creators": [ + "B\u00e9r\u00e9nice Batut", + "Paul Zierep", + "Mina Hojat Ansari", + "Patrick B\u00fchler" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Visualisation", + "Read mapping", + "Genome annotation", + "Local alignment", + "Taxonomic classification", + "Genome comparison", + "Sequence assembly", + "Sequence composition calculation", + "Genome assembly", + "Sequence clustering", + "Sequence assembly validation", + "Genome alignment", + "Sequencing quality control", + "Read binning", + "Validation", + "Query and retrieval", + "Statistical calculation" + ], + "edam_topic": [], + "id": "0563f58718be932d", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=0563f58718be932d", + "name": "MAGs building with individual assembly", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:fairymags", + "name:microgalaxy" + ], + "tools": [ + "maxbin2", + "semibin", + "concoct_cut_up_fasta", + "bowtie2", + "gtdbtk_classify_wf", + "__UNZIP_COLLECTION__", + "coverm_genome", + "fastq_paired_end_joiner", + "checkm_lineage_wf", + "concoct_merge_cut_up_clustering", + "Fasta_to_Contig2Bin", + "metabat2_jgi_summarize_bam_contig_depths", + "concoct_extract_fasta_bins", + "multiqc", + "concoct", + "samtools_sort", + "__FLATTEN__", + "checkm_plot", + "collection_column_join", + "quast", + "concoct_coverage_table", + "metabat2", + "megahit", + "das_tool", + "drep_dereplicate" + ], + "update_time": "2024-12-20", + "versions": 1 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Valerie C. Schiml", + "Magnus \u00d8. Arntzen", + "Francesco Delogu", + "Praveen Kumar", + "Benoit Kunath", + "B\u00e9r\u00e9nice Batut", + " Subina Mehta", + "James E. Johnson", + " Bj\u00f6rn Gr\u00fcning", + "Phillip B. Pope", + "Pratik D. Jagtap", + "Timothy J. Griffin" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Sequence alignment analysis", + "Read pre-processing", + "Sequence comparison", + "Sequence trimming", + "Sequencing quality control", + "Primer removal", + "Sequence similarity search", + "Gene expression profiling", + "Statistical calculation" + ], + "edam_topic": [], + "id": "fd90652d475ed739", + "keep": true, + "latest_version": 6, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", + "name": "MetaT: Metatranscriptomics data analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "metatranscriptomics", + "microbiome" + ], + "tools": [ + "trim_galore", + "bg_sortmerna", + "collection_column_join", + "fastqc", + "__UNZIP_COLLECTION__", + "kallisto_quant" + ], + "update_time": "2024-12-20", + "versions": 6 + }, + { + "create_time": "2024-12-03", + "creators": [ + "Anton Nekrutenko" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Multiple sequence alignment", + "Sequence alignment analysis", + "Phylogenetic tree generation" + ], + "edam_topic": [], + "id": "a2c46deea34d9d80", + "keep": true, + "latest_version": 2, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80", + "name": "Halophiles workup of Comparative gene analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "genome-annotation", + "name:microgalaxy" + ], + "tools": [ + "join1", + "regexColumn1", + "rbc_mafft", + "gops_intersect_1", + "cat1", + "tp_split_on_column", + "bg_diamond", + "Filter1", + "tab2fasta", + "Cut1", + "Add_a_column1", + "rapidnj", + "bg_diamond_view", + "collapse_dataset" + ], + "update_time": "2024-12-05", + "versions": 2 + }, + { + "create_time": "2023-07-02", + "creators": [ + "Engy Nasr", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Read summarisation", + "Validation", + "Sequence alignment", + "RNA-Seq quantification", + "Statistical calculation", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "ca9d3233b0912765", + "keep": true, + "latest_version": 43, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765", + "name": "pAllori Blood RNA", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:pallori", + "name:bloodrna", + "name:umi", + "name:barcode", + "name:transcriptomics" + ], + "tools": [ + "featurecounts", + "__FILTER_FAILED_DATASETS__", + "umi_tools_extract", + "collection_column_join", + "multiqc", + "fastqc", + "rna_star" + ], + "update_time": "2024-11-24", + "versions": 43 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Timothy Griffin", + "Pratik Jagtap", + "James Johnson", + "Clemens Blank", + "Subina Mehta" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Visualisation", + "Prediction and recognition" + ], + "edam_topic": [], + "id": "cefc49c13ff73231", + "keep": true, + "latest_version": 40, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231", + "name": "Metaproteomics workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:metaproteomics", + "name:galaxyp", + "name:massspectrometry", + "name:microgalaxy" + ], + "tools": [ + "sqlite_to_tabular", + "query_tabular", + "unipept", + "search_gui", + "peptide_shaker" + ], + "update_time": "2024-11-21", + "versions": 40 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Johannes Effenberger" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "6239178d7cc4ac68", + "keep": true, + "latest_version": 5, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68", + "name": "Feature-Count Table Normalization", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "normalization", + "softmax", + "relative-abundance", + "sigmoid", + "css", + "limma-tmm", + "limma-rle" + ], + "tools": [ + "map_param_value", + "__BUILD_LIST__", + "__EXTRACT_DATASET__", + "__FILTER_EMPTY_DATASETS__", + "Grep1" + ], + "update_time": "2024-11-21", + "versions": 5 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Subina Metha", + "Timothy J. Griffin", + "Pratik Jagtap", + "Emma Leith", + "Marie Crane" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Visualisation", + "Label-free quantification", + "Filtering", + "Prediction and recognition", + "Formatting" + ], + "edam_topic": [], + "id": "cd675ab32d3e7833", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833", + "name": "metaQuantome_datacreation_workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "proteomics", + "name:microgalaxy" + ], + "tools": [ + "tp_replace_in_column", + "Remove beginning1", + "regex1", + "Filter1", + "Cut1", + "msconvert", + "query_tabular", + "tp_replace_in_line", + "unipept", + "search_gui", + "flashlfq", + "peptide_shaker" + ], + "update_time": "2024-11-21", + "versions": 1 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Subina Mehta", + "Timothy J. Griffin", + "Pratik Jagtap", + "Emma Leith", + "Marie Crane", + "Praveen Kumar" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Statistical inference", + "Functional clustering", + "Visualisation", + "Principal component visualisation", + "Indexing", + "Quantification", + "Query and retrieval", + "Differential protein expression analysis", + "Heat map generation", + "Filtering" + ], + "edam_topic": [], + "id": "e5a89ef7b5f1c1d9", + "keep": true, + "latest_version": 3, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9", + "name": "metaquantome-function-worklow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "proteomics", + "name:microgalaxy" + ], + "tools": [ + "metaquantome_db", + "metaquantome_viz", + "metaquantome_expand", + "metaquantome_stat", + "metaquantome_filter", + "metaquantome_sample" + ], + "update_time": "2024-11-21", + "versions": 3 + }, + { + "create_time": "2023-06-30", + "creators": [ + "Engy Nasr", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Read pre-processing", + "Visualisation", + "Sequence feature detection", + "Aggregation", + "Sequence trimming", + "Sequencing quality control", + "Analysis", + "Primer removal", + "Validation", + "Taxonomic classification", + "Statistical calculation", + "DNA barcoding" + ], + "edam_topic": [], + "id": "466bdd8ba7b67264", + "keep": true, + "latest_version": 70, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", + "name": "pAllori Amplicon 16S Pre-Processing and Taxonomy Classification", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:16s", + "name:metagenomics", + "name:pallori" + ], + "tools": [ + "cutadapt", + "trimmomatic", + "tp_cut_tool", + "kraken2", + "__FLATTEN__", + "unzip", + "multiqc", + "fastqc", + "taxonomy_krona_chart", + "collection_column_join", + "lotus2", + "ampvis2_heatmap", + "ampvis2_load", + "ampvis2_ordinate", + "krakentools_kreport2krona" + ], + "update_time": "2024-11-21", + "versions": 70 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr ", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Taxonomic classification", + "Cross-assembly", + "Expression analysis", + "Read mapping" + ], + "edam_topic": [], + "id": "c09159d7aad0f264", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264", + "name": "Cloud Aerosol MT-MG Contamination Filtering", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "recentrifuge", + "kraken2", + "bowtie2", + "seq_filter_by_id", + "fastq_to_tabular", + "filter_tabular" + ], + "update_time": "2024-11-21", + "versions": 2 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Read summarisation", + "Validation", + "RNA-Seq quantification", + "Sequencing quality control", + "Read mapping" + ], + "edam_topic": [], + "id": "63478edcea3f449a", + "keep": true, + "latest_version": 4, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=63478edcea3f449a", + "name": " Cloud-Aerosole MT-MG Functional Profiling", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "featurecounts", + "bowtie2", + "multiqc" + ], + "update_time": "2024-11-21", + "versions": 4 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Validation", + "Statistical calculation", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "1ef76b7b86e15792", + "keep": true, + "latest_version": 6, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792", + "name": "Cloud-Aerosole MT-MG Pre-Processing", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "trimmomatic", + "multiqc", + "fastqc" + ], + "update_time": "2024-11-21", + "versions": 6 + }, + { + "create_time": "2024-10-31", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Variant calling", + "Pairwise sequence alignment" + ], + "edam_topic": [], + "id": "64abcddeb516a712", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=64abcddeb516a712", + "name": "Allele-based Pathogen Identification (release v0.1.2)", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:collection", + "name:microgalaxy", + "name:pathogfair", + "name:iwc" + ], + "tools": [ + "tp_head_tool", + "clair3", + "samtools_depth", + "snpSift_filter", + "regexColumn1", + "Remove beginning1", + "bcftools_norm", + "tp_cut_tool", + "table_compute", + "bcftools_consensus", + "samtools_coverage", + "minimap2", + "Count1", + "Cut1", + "Paste1", + "CONVERTER_gz_to_uncompressed", + "snpSift_extractFields", + "collapse_dataset" + ], + "update_time": "2024-10-31", + "versions": 1 + }, + { + "create_time": "2023-10-10", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "011f701c5a55bfdf", + "keep": true, + "latest_version": 128, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf", + "name": "Mgnify ML", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy" + ], + "tools": [ + "__BUILD_LIST__", + "interactive_tool_jupyter_notebook" + ], + "update_time": "2024-03-15", + "versions": 128 + }, + { + "create_time": "2023-12-14", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence alignment", + "Mapping", + "Read mapping" + ], + "edam_topic": [], + "id": "0e492839192d26e0", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=0e492839192d26e0", + "name": "Ecoli Comparison", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "assembly", + "name:microgalaxy" + ], + "tools": [ + "cat1", + "Cut1", + "datamash_ops", + "collapse_dataset", + "lastz_wrapper_2", + "tp_cat", + "Grep1", + "fasta_compute_length", + "addValue", + "bedtools_sortbed", + "join1", + "bedtools_complementbed", + "tp_grep_tool", + "random_lines1", + "bedtools_intersectbed", + "fasta_filter_by_length", + "mergeCols1", + "tp_sed_tool", + "tp_sort_header_tool", + "Filter1" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-14", + "creators": [ + "Anton Nekrutenko" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Multiple sequence alignment", + "Sequence alignment analysis", + "Phylogenetic tree generation" + ], + "edam_topic": [], + "id": "86900be4282d4b1d", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d", + "name": "Comparative gene analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "vgp", + "genome-annotation", + "name:microgalaxy" + ], + "tools": [ + "join1", + "regexColumn1", + "rbc_mafft", + "gops_intersect_1", + "cat1", + "tp_split_on_column", + "bg_diamond", + "Filter1", + "tab2fasta", + "Cut1", + "Add_a_column1", + "rapidnj", + "bg_diamond_view", + "collapse_dataset" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-14", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Genome visualisation" + ], + "edam_topic": [], + "id": "3c233cc56d4df8b0", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0", + "name": "Apollo Load Test", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "genome-annotation", + "name:microgalaxy" + ], + "tools": [ + "list_organism", + "create_or_update", + "iframe", + "jbrowse", + "create_account" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-14", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Sequence analysis", + "Sequence assembly", + "Variant calling", + "Sequence visualisation", + "Sequence assembly visualisation", + "Pairwise sequence alignment", + "Scatter plot plotting", + "Genome visualisation", + "Genome assembly", + "Gene prediction", + "Base-calling", + "Cross-assembly", + "De-novo assembly", + "Genome annotation", + "Coding region prediction", + "Box-Whisker plot plotting", + "Mapping assembly" + ], + "edam_topic": [], + "id": "152223c8aed27357", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=152223c8aed27357", + "name": "Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL)", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "wmdi", + "name:microgalaxy" + ], + "tools": [ + "circos_wiggle_to_scatter", + "trimmomatic", + "circos_interval_to_tile", + "tab2fasta", + "jbrowse", + "Cut1", + "tp_text_file_with_recurring_lines", + "bandage_image", + "bg_column_arrange_by_header", + "tp_cat", + "flye", + "gff2bed1", + "Grep1", + "fasta_compute_length", + "minimap2", + "tbl2gff3", + "prokka", + "circos", + "Add_a_column1", + "staramr_search", + "regex1", + "PlasFlow", + "ncbi_blastn_wrapper", + "tp_head_tool", + "join1", + "circos_gc_skew", + "tp_split_on_column", + "tp_easyjoin_tool", + "fasta2tab", + "deeptools_bam_coverage", + "regex_replace", + "tp_cut_tool", + "tp_sort_header_tool", + "Filter1", + "nanoplot", + "medaka_consensus_pipeline" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-14", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "6d333ed886aab471", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=6d333ed886aab471", + "name": "From VCFs to SNP distance matrix", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "evolution", + "name:microgalaxy" + ], + "tools": [ + "tp_cat", + "snp_sites", + "tb_variant_filter", + "bcftools_consensus", + "snp_dists" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-14", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Phylogenetic tree generation", + "Phylogenetic tree visualisation", + "Variant calling" + ], + "edam_topic": [], + "id": "3a8fde248a4d0383", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383", + "name": "From Fastqs to VCFs and BAMs", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "evolution", + "name:microgalaxy" + ], + "tools": [ + "tb_variant_filter", + "snippy", + "trimmomatic", + "__MERGE_COLLECTION__" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-14", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Antimicrobial resistance prediction" + ], + "edam_topic": [], + "id": "d0d6dae0d1eecc21", + "keep": true, + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21", + "name": "From BAMs to drug resistance prediction with TB-profiler", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "evolution", + "name:microgalaxy" + ], + "tools": [ + "tp_cat", + "tp_sed_tool", + "tp_grep_tool", + "samtools_view", + "tb_profiler_profile", + "tp_replace_in_line", + "addName", + "__MERGE_COLLECTION__" + ], + "update_time": "2023-12-14", + "versions": 0 + }, + { + "create_time": "2023-12-13", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Variant calling", + "Statistical calculation", + "Read mapping" + ], + "edam_topic": [], + "id": "21a39ac4c1becb31", + "keep": true, + "latest_version": 2, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31", + "name": "Compute Allel Frequency Table from paired reads", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "hpylori" + ], + "tools": [ + "freebayes", + "snpSift_filter", + "bcftools_view", + "bcftools_norm", + "bowtie2", + "tp_awk_tool", + "vcf2tsv" + ], + "update_time": "2023-12-13", + "versions": 2 + }, + { + "create_time": "2023-10-27", + "creators": [], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Variant calling", + "Statistical calculation", + "Read mapping" + ], + "edam_topic": [], + "id": "61fe08fb3d5e83f8", + "keep": true, + "latest_version": 13, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8", + "name": "Reference genome choice (indels, coverage, depth) for short reads", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "hpylori" + ], + "tools": [ + "vcf2tsv", + "freebayes", + "tp_cat", + "samtools_depth", + "bcftools_norm", + "bowtie2", + "samtools_coverage", + "collection_element_identifiers", + "collapse_dataset" + ], + "update_time": "2023-12-13", + "versions": 13 + } +] \ No newline at end of file diff --git a/communities/microgalaxy/resources/curated_workflows.tsv b/communities/microgalaxy/resources/curated_workflows.tsv index 3bf2b82f..58ced4bc 100644 --- a/communities/microgalaxy/resources/curated_workflows.tsv +++ b/communities/microgalaxy/resources/curated_workflows.tsv @@ -1,8 +1,25 @@ Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +clinicalmp-discovery/main WorkflowHub 1225 https://workflowhub.eu/workflows/1225?version=1 Subina Mehta 2024-12-10 2025-01-13 1 1 24.0 tp_cat, Grep1, fasta2tab, dbbuilder, Remove beginning1, maxquant, Filter1, Cut1, msconvert, query_tabular, fasta_cli, fasta_merge_files_and_filter_unique_sequences, search_gui, Grouping1, ident_params, filter_tabular, peptide_shaker Protein quantification, Filtering, Imputation, Visualisation, Principal component plotting, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation, Formatting CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-data-interpretation/main WorkflowHub 1219 https://workflowhub.eu/workflows/1219?version=1 GalaxyP 2024-11-26 2024-12-06 1 1 6.0 msstatstmt, Grep1, unipept Visualisation, Prediction and recognition CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-verification/main WorkflowHub 1218 https://workflowhub.eu/workflows/1218?version=1 Pratik Jagtap 2024-11-26 2024-12-06 1 1 19.0 tp_cat, Remove beginning1, dbbuilder, pepquery2, Filter1, Cut1, query_tabular, uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences, Grouping1, collapse_dataset CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-database-generation/main WorkflowHub 1216 https://workflowhub.eu/workflows/1216?version=1 Subina Mehta 2024-11-23 2024-12-06 1 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences de Novo sequencing, Tag-based peptide identification, Protein identification, Target-Decoy, Expression analysis CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-quantitation/main WorkflowHub 1177 https://workflowhub.eu/workflows/1177?version=1 GalaxyP 2024-10-07 2024-10-07 1 1 7.0 "extracting microbial Peptides +Grep1, extract peptides +Cut1, maxquant, extract proteins +Cut1, extracting microbial Proteins +Grep1, Quantified-Peptides +Grouping1, Quantified-Proteins +Grouping1" Protein quantification, Imputation, Visualisation, Principal component plotting, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=7 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2024-11-26 2024-11-26 7 7 7.0 tooldistillator, bandage_info, tooldistillator_summarize, shovill, quast, refseq_masher_matches, bandage_image Sequence assembly visualisation, Data handling, Genome assembly, Parsing, Sequence assembly validation, Visualisation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=8 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2024-11-23 2024-11-23 8 8 6.0 recentrifuge, tooldistillator, tooldistillator_summarize, kraken2, fastp, est_abundance Data handling, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Parsing, Cross-assembly, Expression analysis, Sequencing quality control GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub 1090 https://workflowhub.eu/workflows/1090?version=2 Debjyoti Ghosh 2024-11-26 2024-12-06 2 2 3.0 Rarefaction, Taxonomic analysis, Phylogenetic tree for diversity analysis MIT Intergalactic Workflow Commission (IWC) True False +allele-based-pathogen-identification/main WorkflowHub 1063 https://workflowhub.eu/workflows/1063?version=3 Engy Nasr, Bérénice Batut, Paul Zierep 2024-10-30 2024-10-31 3 3 23.0 tp_head_tool, clair3, samtools_depth, snpSift_filter, regexColumn1, Remove beginning1, bcftools_norm, tp_cut_tool, table_compute, bcftools_consensus, samtools_coverage, minimap2, Count1, Cut1, Paste1, CONVERTER_gz_to_uncompressed, snpSift_extractFields, collapse_dataset Variant calling, Pairwise sequence alignment MIT Intergalactic Workflow Commission (IWC) True False +gene-based-pathogen-identification/main WorkflowHub 1062 https://workflowhub.eu/workflows/1062?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 1 1 15.0 __BUILD_LIST__, flye, abricate, compose_text_param, tp_find_and_replace, tab2fasta, param_value_from_file, collection_element_identifiers, medaka_consensus_pipeline, bandage_image, fasta2tab, split_file_to_collection Antimicrobial resistance prediction, Sequence assembly, Variant calling, Sequence assembly visualisation, Base-calling, Genome assembly, Cross-assembly, De-novo assembly, Mapping assembly MIT 10.48546/workflowhub.workflow.1062.1 Intergalactic Workflow Commission (IWC) True False +pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub 1060 https://workflowhub.eu/workflows/1060?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 1 1 60.0 tp_replace_in_column, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, clustalw, tab2fasta, Cut1, collapse_dataset, __FILTER_FAILED_DATASETS__, Remove beginning1, Count1, bedtools_getfastabed, Grouping1, regex1, regexColumn1, tp_split_on_column, fasttree, ggplot2_heatmap, newick_display, fasta2tab, collection_column_join, fasta_merge_files_and_filter_unique_sequences, tp_multijoin_tool Phylogenetic tree analysis, Phylogenetic tree generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree reconstruction, Visualisation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Mapping MIT 10.48546/workflowhub.workflow.1060.1 Intergalactic Workflow Commission (IWC) True False +taxonomy-profiling-and-visualization-with-krona/main WorkflowHub 1059 https://workflowhub.eu/workflows/1059?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 1 1 3.0 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT 10.48546/workflowhub.workflow.1059.1 Intergalactic Workflow Commission (IWC) True False bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2024-10-26 2024-10-26 9 9 6.0 tooldistillator, tooldistillator_summarize, integron_finder, isescan, plasmidfinder, bakta Structural variation detection, Nucleic acid feature detection, Protein feature detection, Genome assembly, Parsing, Sequence motif recognition, Genome annotation, Data handling, Multilocus sequence typing, Scaffolding GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=7 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2024-10-26 2024-10-27 7 7 5.0 abricate, tooldistillator, tooldistillator_summarize, amrfinderplus, staramr_search Antimicrobial resistance prediction, Data handling, Parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +dada2/main WorkflowHub 790 https://workflowhub.eu/workflows/790?version=2 Matthias Bernt name:amplicon 2024-05-30 2024-06-02 2 2 14.0 dada2_plotQualityProfile, dada2_filterAndTrim, __APPLY_RULES__, dada2_mergePairs, dada2_seqCounts, dada2_learnErrors, dada2_dada, dada2_assignTaxonomyAddspecies, dada2_removeBimeraDenovo, __UNZIP_COLLECTION__, dada2_makeSequenceTable Variant calling, DNA barcoding MIT Intergalactic Workflow Commission (IWC) True False pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=2 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2024-06-22 2024-06-22 2 2 40.0 " __FLATTEN__, __ZIP_COLLECTION__, datamash_ops, tp_cat, compose_text_param, @@ -12,6 +29,7 @@ pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?ver __APPLY_RULES__, EMBOSS: maskseq51, multiqc, ivar_trim, fastp, split_file_to_collection, samtools_stats, Grep1, samtools_merge, tp_sed_tool, collection_element_identifiers, __FILTER_FAILED_DATASETS__, bwa_mem" Sequence analysis, Sequence alignment analysis, Generation, Sequence alignment, Sequencing quality control, Read mapping, Validation, Local alignment, Sequence contamination filtering, Genome indexing, Global alignment MIT Intergalactic Workflow Commission (IWC) True False +Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub 749 https://workflowhub.eu/workflows/749?version=1 Anthony Bretaudeau genome-annotation 2024-02-14 2024-02-15 1 1 5.0 list_organism, create_or_update, iframe, jbrowse, create_account Genome visualisation CC-BY-4.0 EuroScienceGateway True False GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2023-02-13 1 1 12.0 PlasFlow, miniasm, unicycler, gfa_to_fa, minimap2, racon, nanoplot, bandage_image, staramr_search Sequence analysis, Scatter plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Genome assembly, Aggregation, De-novo assembly, Box-Whisker plot plotting, Mapping assembly Microbiology CC-BY-4.0 Galaxy Training Network True False 3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2023-02-13 1 1 2.0 fastp, shovill Sequence contamination filtering, Genome assembly, Sequencing quality control Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False 2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2023-02-13 1 1 7.0 ncbi_blastn_wrapper, shovill, minimap2, ngsutils_bam_filter, samtools_stats, fasta_merge_files_and_filter_unique_sequences, picard_SamToFastq Variant calling, Pairwise sequence alignment, Sequence contamination filtering, Read pre-processing, Genome assembly, Formatting, Sequencing quality control Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False @@ -30,10 +48,17 @@ Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 2.0 mothur_classify_seqs, mothur_remove_lineage Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 QCIF Bioinformatics True False Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_summary_seqs, mothur_screen_seqs, mothur_unique_seqs, mothur_count_seqs Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 QCIF Bioinformatics True False Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 9.0 mothur_screen_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_remove_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_pre_cluster Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 QCIF Bioinformatics True False +TB Variant Analysis v1.0 WorkflowHub 1035 https://workflowhub.eu/workflows/1035?version=1 Peter van Heusden pathogen, tuberculosis 2024-06-07 2024-06-12 1 1 15.0 tb_variant_filter, snippy, qualimap_bamqc, kraken2, tp_sed_tool, __FLATTEN__, bcftools_consensus, tbvcfreport, multiqc, fastp, EMBOSS: seqret84, tb_profiler_profile, mosdepth, tp_awk_tool Sequence analysis, Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence alignment, Phylogenetic tree visualisation, Taxonomic classification, Sequencing quality control, Validation, Local alignment, Sequence contamination filtering, Phylogenetic tree generation, Global alignment Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later SANBI Pathogen Bioinformatics True False +Workflow 3: AMR - SeqSero2/SISTR WorkflowHub 407 https://workflowhub.eu/workflows/407?version=1 bioinformatics, antimicrobial resistance 2022-11-24 2024-09-09 1 1 14.0 bbtools_tadpole, shovill, bbtools_bbduk, seqsero2, hamronize_tool, hamronize_summarize, __UNZIP_COLLECTION__, sistr_cmd, kma_map, mob_recon, srst2 Antimicrobial resistance prediction, RNA-Seq analysis, Sequence alignment, Genome assembly, Visualisation, Parsing, Sequence trimming, Read mapping, Genome alignment, Read binning, Data handling, Sequence contamination filtering, Genome indexing, Multilocus sequence typing GPL-3.0 Seq4AMR True False +Workflow 2: Sciensano WorkflowHub 644 https://workflowhub.eu/workflows/644?version=1 2023-11-07 2024-09-09 1 1 1.0 pipeline_stec_1.0 CC-BY-4.0 Seq4AMR True False Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2024-09-09 1 1 10.0 abricate, tp_find_and_replace, shovill, hamronize_tool, hamronize_summarize, collapse_dataset, staramr_search Antimicrobial resistance prediction, Data handling, Genome assembly, Parsing GPL-3.0 Seq4AMR True False +Workflow 1: AbritAMR WorkflowHub 634 https://workflowhub.eu/workflows/634?version=1 2023-10-31 2024-09-09 1 1 1.0 abritamr Antimicrobial resistance prediction CC-BY-4.0 Seq4AMR True False AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2024-12-24 2 2 36.0 , cat1, __APPLY_RULES__, Cut1, tp_text_file_with_recurring_lines, datamash_ops, collapse_dataset, Grep1, tp_find_and_replace, addValue, __MERGE_COLLECTION__, staramr_search, tp_split_on_column, shovill, hamronize_summarize, cat_multi_datasets, abricate, cast, hamronize_tool Antimicrobial resistance prediction, Data handling, Genome assembly, Parsing MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False Query a metaplasmidome database to identify and annotate plasmids in metagenomes dev.WorkflowHub 1380 https://dev.workflowhub.eu/workflows/1380?version=1 gtn, galaxy, metaplasmidome, name:microgalaxy, metagenomics 2025-01-13 2025-01-20 1 1 47.0 MQoutputfilter, join1, tp_replace_in_column, ggplot2_histogram, cat1, sort1, tp_sorted_uniq, CONVERTER_fasta_to_tabular, minimap2, count_gff_features, Filter1, tab2fasta, Cut1, Add_a_column1, tp_tail_tool, add_column_headers, Grouping1, histogram_rpy Visualisation, Pairwise sequence alignment MIT Galaxy Training Network True False Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' dev.WorkflowHub 1366 https://dev.workflowhub.eu/workflows/1366?version=1 fungi, gtn, galaxy, lotus2, ecology, metagenomics 2024-10-07 2024-10-07 1 1 1.0 lotus2 Sequence feature detection, DNA barcoding MIT Galaxy Training Network True False +Calculating diversity from microbiome taxonomic data dev.WorkflowHub 1349 https://dev.workflowhub.eu/workflows/1349?version=1 gtn, galaxy, name:gtn 2024-08-12 2024-10-07 1 1 6.0 krakentools_beta_diversity, krakentools_alpha_diversity Visualisation, Aggregation MIT Galaxy Training Network True False +Quality and contamination control in bacterial isolate using Illumina MiSeq Data dev.WorkflowHub 1344 https://dev.workflowhub.eu/workflows/1344?version=1 gtn, galaxy, sequence-analysis 2024-07-15 2024-10-07 1 1 6.0 recentrifuge, kraken2, fastqc, fastp, est_abundance Sequence composition calculation, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Cross-assembly, Expression analysis, Sequencing quality control GPL-3.0-or-later Galaxy Training Network True False +Checking expected species and contamination in bacterial isolate dev.WorkflowHub 1217 https://dev.workflowhub.eu/workflows/1217?version=2 gtn, galaxy, ecology 2024-07-16 2024-10-07 2 2 3.0 kraken2, recentrifuge, est_abundance Taxonomic classification, Cross-assembly, Statistical calculation, Expression analysis GPL-3.0-or-later Galaxy Training Network True False Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1133 https://dev.workflowhub.eu/workflows/1133?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 6.0 mothur_classify_otu, mothur_remove_groups, mothur_sub_sample, mothur_count_groups, mothur_make_shared, mothur_cluster_split Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1129 https://dev.workflowhub.eu/workflows/1129?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_rarefaction_single, mothur_summary_single, XY_Plot_1 Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1125 https://dev.workflowhub.eu/workflows/1125?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 4.0 mothur_dist_seqs, mothur_rarefaction_single, mothur_make_shared, mothur_cluster Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False @@ -46,7 +71,9 @@ Training: 16S rRNA Sequencing With Mothur: Main Tutorial dev.WorkflowHub 1101 ht Identification of the micro-organisms in a beer using Nanopore sequencing dev.WorkflowHub 1097 https://dev.workflowhub.eu/workflows/1097?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 8.0 porechop, kraken2, Filter1, fastqc, fastp, taxonomy_krona_chart, krakentools_kreport2krona Sequence composition calculation, Visualisation, Sequence contamination filtering, Taxonomic classification, Aggregation, Statistical calculation, Sequencing quality control MIT Galaxy Training Network True False Taxonomic Profiling and Visualization of Metagenomic Data dev.WorkflowHub 1095 https://dev.workflowhub.eu/workflows/1095?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 10.0 metaphlan, kraken2, interactive_tool_pavian, interactive_tool_phinch, est_abundance, __UNZIP_COLLECTION__, kraken_biom, taxonomy_krona_chart, krakentools_kreport2krona Phylogenetic tree analysis, Nucleic acid sequence analysis, Visualisation, Taxonomic classification, Aggregation, Statistical calculation MIT Galaxy Training Network True False Workflow 3: Functional Information (quick) dev.WorkflowHub 1080 https://dev.workflowhub.eu/workflows/1080?version=1 gtn, galaxy, asaim, metagenomics 2024-06-25 2024-10-07 1 1 12.0 humann_regroup_table, Grep1, humann_split_stratified_table, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_unpack_pathways, humann_rename_table, humann_renorm_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT Galaxy Training Network True False +pox-virus-tiled-amplicon-ref-masking dev.WorkflowHub 1078 https://dev.workflowhub.eu/workflows/1078?version=1 gtn, galaxy, variant-analysis 2024-06-25 2024-10-07 1 1 14.0 compose_text_param, Grep1, fasta_compute_length, EMBOSS: maskseq51, Cut1, Add_a_column1, param_value_from_file, datamash_ops Sequence analysis, Sequence alignment analysis, Local alignment, Sequence alignment, Global alignment MIT Galaxy Training Network True False Amplicon Tutorial dev.WorkflowHub 1070 https://dev.workflowhub.eu/workflows/1070?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 17.0 krona-text, mothur_screen_seqs, mothur_unique_seqs, mothur_classify_otu, mothur_filter_seqs, mothur_cluster_split, mothur_merge_files, mothur_make_biom, mothur_count_seqs, mothur_make_shared, mothur_make_group, mothur_summary_seqs, mothur_classify_seqs, mothur_align_seqs, mothur_pre_cluster Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 Galaxy Training Network True False +TB Variant Analysis v1.0 dev.WorkflowHub 1069 https://dev.workflowhub.eu/workflows/1069?version=2 gtn, galaxy, pathogen, tuberculosis 2024-07-16 2024-10-07 2 2 15.0 tb_variant_filter, snippy, qualimap_bamqc, kraken2, tp_sed_tool, __FLATTEN__, bcftools_consensus, tbvcfreport, multiqc, fastp, EMBOSS: seqret84, tb_profiler_profile, mosdepth, tp_awk_tool Sequence analysis, Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence alignment, Phylogenetic tree visualisation, Taxonomic classification, Sequencing quality control, Validation, Local alignment, Sequence contamination filtering, Phylogenetic tree generation, Global alignment AGPL-3.0-or-later Galaxy Training Network True False "WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" dev.WorkflowHub 1067 https://dev.workflowhub.eu/workflows/1067?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 7.0 metaphlan2, humann2, taxonomy_krona_chart, humann2_renorm_table, humann2_regroup_table, metaphlan2krona Visualisation CC-BY-4.0 Galaxy Training Network True False Training: 16S rRNA Analysis with Nanopore Sequencing Reads dev.WorkflowHub 1064 https://dev.workflowhub.eu/workflows/1064?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 11.0 datamash_reverse, porechop, Remove beginning1, kraken2, multiqc, fastqc, fastp, tp_replace_in_line, taxonomy_krona_chart Sequence composition calculation, Validation, Visualisation, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Sequencing quality control CC-BY-4.0 Galaxy Training Network True False Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1060 https://dev.workflowhub.eu/workflows/1060?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False diff --git a/communities/microgalaxy/resources/tag_filtered_workflows.json b/communities/microgalaxy/resources/tag_filtered_workflows.json index 1dea6608..2833f56b 100644 --- a/communities/microgalaxy/resources/tag_filtered_workflows.json +++ b/communities/microgalaxy/resources/tag_filtered_workflows.json @@ -1,4 +1,58 @@ [ + { + "create_time": "2024-12-10", + "creators": [ + "Subina Mehta" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Protein quantification", + "Filtering", + "Imputation", + "Visualisation", + "Principal component plotting", + "Clustering", + "Standardisation and normalisation", + "Heat map generation", + "Statistical calculation", + "Formatting" + ], + "edam_topic": [], + "id": "1225", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1225?version=1", + "name": "clinicalmp-discovery/main", + "number_of_steps": 24, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "tp_cat", + "Grep1", + "fasta2tab", + "dbbuilder", + "Remove beginning1", + "maxquant", + "Filter1", + "Cut1", + "msconvert", + "query_tabular", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", + "search_gui", + "Grouping1", + "ident_params", + "filter_tabular", + "peptide_shaker" + ], + "update_time": "2025-01-13", + "versions": 1 + }, { "create_time": "2024-12-10", "creators": [ @@ -57,6 +111,109 @@ "update_time": "2024-12-10", "versions": 2 }, + { + "create_time": "2024-11-26", + "creators": [ + "GalaxyP" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Prediction and recognition" + ], + "edam_topic": [], + "id": "1219", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1219?version=1", + "name": "clinicalmp-data-interpretation/main", + "number_of_steps": 6, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "msstatstmt", + "Grep1", + "unipept" + ], + "update_time": "2024-12-06", + "versions": 1 + }, + { + "create_time": "2024-11-26", + "creators": [ + "Pratik Jagtap" + ], + "deprecated": false, + "doi": null, + "edam_operation": [], + "edam_topic": [], + "id": "1218", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1218?version=1", + "name": "clinicalmp-verification/main", + "number_of_steps": 19, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "tp_cat", + "Remove beginning1", + "dbbuilder", + "pepquery2", + "Filter1", + "Cut1", + "query_tabular", + "uniprotxml_downloader", + "fasta_merge_files_and_filter_unique_sequences", + "Grouping1", + "collapse_dataset" + ], + "update_time": "2024-12-06", + "versions": 1 + }, + { + "create_time": "2024-11-23", + "creators": [ + "Subina Mehta" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "de Novo sequencing", + "Tag-based peptide identification", + "Protein identification", + "Target-Decoy", + "Expression analysis" + ], + "edam_topic": [], + "id": "1216", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1216?version=1", + "name": "clinicalmp-database-generation/main", + "number_of_steps": 3, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "metanovo", + "fasta_merge_files_and_filter_unique_sequences" + ], + "update_time": "2024-12-06", + "versions": 1 + }, { "create_time": "2024-11-14", "creators": [ @@ -114,6 +271,48 @@ "update_time": "2024-12-24", "versions": 2 }, + { + "create_time": "2024-10-07", + "creators": [ + "GalaxyP" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Protein quantification", + "Imputation", + "Visualisation", + "Principal component plotting", + "Clustering", + "Standardisation and normalisation", + "Heat map generation", + "Statistical calculation" + ], + "edam_topic": [], + "id": "1177", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1177?version=1", + "name": "clinicalmp-quantitation/main", + "number_of_steps": 7, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "extracting microbial Peptides\nGrep1", + "extract peptides\nCut1", + "maxquant", + "extract proteins\nCut1", + "extracting microbial Proteins\nGrep1", + "Quantified-Peptides\nGrouping1", + "Quantified-Proteins\nGrouping1" + ], + "update_time": "2024-10-07", + "versions": 1 + }, { "create_time": "2024-11-26", "creators": [ @@ -216,6 +415,84 @@ "update_time": "2024-11-23", "versions": 8 }, + { + "create_time": "2022-11-24", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Antimicrobial resistance prediction", + "RNA-Seq analysis", + "Sequence alignment", + "Genome assembly", + "Visualisation", + "Parsing", + "Sequence trimming", + "Read mapping", + "Genome alignment", + "Read binning", + "Data handling", + "Sequence contamination filtering", + "Genome indexing", + "Multilocus sequence typing" + ], + "edam_topic": [], + "id": "407", + "keep": true, + "latest_version": 1, + "license": "GPL-3.0", + "link": "https://workflowhub.eu/workflows/407?version=1", + "name": "Workflow 3: AMR - SeqSero2/SISTR", + "number_of_steps": 14, + "projects": [ + "Seq4AMR" + ], + "source": "WorkflowHub", + "tags": [ + "bioinformatics", + "antimicrobial resistance" + ], + "tools": [ + "bbtools_tadpole", + "shovill", + "bbtools_bbduk", + "seqsero2", + "hamronize_tool", + "hamronize_summarize", + "__UNZIP_COLLECTION__", + "sistr_cmd", + "kma_map", + "mob_recon", + "srst2" + ], + "update_time": "2024-09-09", + "versions": 1 + }, + { + "create_time": "2023-11-07", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [], + "edam_topic": [], + "id": "644", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/644?version=1", + "name": "Workflow 2: Sciensano", + "number_of_steps": 1, + "projects": [ + "Seq4AMR" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "pipeline_stec_1.0" + ], + "update_time": "2024-09-09", + "versions": 1 + }, { "create_time": "2023-05-11", "creators": [], @@ -259,103 +536,492 @@ "versions": 1 }, { - "create_time": "2024-10-26", + "create_time": "2023-10-31", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Antimicrobial resistance prediction" + ], + "edam_topic": [], + "id": "634", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/634?version=1", + "name": "Workflow 1: AbritAMR", + "number_of_steps": 1, + "projects": [ + "Seq4AMR" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "abritamr" + ], + "update_time": "2024-09-09", + "versions": 1 + }, + { + "create_time": "2024-11-26", "creators": [ - "ABRomics None", - "Pierre Marin", - "Clea Siguret" + "Debjyoti Ghosh" ], "deprecated": false, "doi": null, - "edam_operation": [ - "Structural variation detection", - "Nucleic acid feature detection", - "Protein feature detection", - "Genome assembly", - "Parsing", - "Sequence motif recognition", + "edam_operation": [], + "edam_topic": [], + "id": "1090", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/1090?version=2", + "name": "qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis", + "number_of_steps": 3, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "Rarefaction", + "Taxonomic analysis", + "Phylogenetic tree for diversity analysis" + ], + "update_time": "2024-12-06", + "versions": 2 + }, + { + "create_time": "2024-10-30", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Paul Zierep" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Variant calling", + "Pairwise sequence alignment" + ], + "edam_topic": [], + "id": "1063", + "keep": true, + "latest_version": 3, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/1063?version=3", + "name": "allele-based-pathogen-identification/main", + "number_of_steps": 23, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "tp_head_tool", + "clair3", + "samtools_depth", + "snpSift_filter", + "regexColumn1", + "Remove beginning1", + "bcftools_norm", + "tp_cut_tool", + "table_compute", + "bcftools_consensus", + "samtools_coverage", + "minimap2", + "Count1", + "Cut1", + "Paste1", + "CONVERTER_gz_to_uncompressed", + "snpSift_extractFields", + "collapse_dataset" + ], + "update_time": "2024-10-31", + "versions": 3 + }, + { + "create_time": "2024-06-26", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Paul Zierep" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.1062.1", + "edam_operation": [ + "Antimicrobial resistance prediction", + "Sequence assembly", + "Variant calling", + "Sequence assembly visualisation", + "Base-calling", + "Genome assembly", + "Cross-assembly", + "De-novo assembly", + "Mapping assembly" + ], + "edam_topic": [], + "id": "1062", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/1062?version=1", + "name": "gene-based-pathogen-identification/main", + "number_of_steps": 15, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "__BUILD_LIST__", + "flye", + "abricate", + "compose_text_param", + "tp_find_and_replace", + "tab2fasta", + "param_value_from_file", + "collection_element_identifiers", + "medaka_consensus_pipeline", + "bandage_image", + "fasta2tab", + "split_file_to_collection" + ], + "update_time": "2024-07-15", + "versions": 1 + }, + { + "create_time": "2024-06-26", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Paul Zierep" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.1060.1", + "edam_operation": [ + "Phylogenetic tree analysis", + "Phylogenetic tree generation", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Phylogenetic tree reconstruction", + "Visualisation", + "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", + "Mapping" + ], + "edam_topic": [], + "id": "1060", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/1060?version=1", + "name": "pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main", + "number_of_steps": 60, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "tp_replace_in_column", + "__FILTER_EMPTY_DATASETS__", + "tp_sorted_uniq", + "clustalw", + "tab2fasta", + "Cut1", + "collapse_dataset", + "__FILTER_FAILED_DATASETS__", + "Remove beginning1", + "Count1", + "bedtools_getfastabed", + "Grouping1", + "regex1", + "regexColumn1", + "tp_split_on_column", + "fasttree", + "ggplot2_heatmap", + "newick_display", + "fasta2tab", + "collection_column_join", + "fasta_merge_files_and_filter_unique_sequences", + "tp_multijoin_tool" + ], + "update_time": "2024-07-15", + "versions": 1 + }, + { + "create_time": "2024-06-26", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Paul Zierep" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.1059.1", + "edam_operation": [ + "Visualisation", + "Taxonomic classification", + "Aggregation" + ], + "edam_topic": [], + "id": "1059", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/1059?version=1", + "name": "taxonomy-profiling-and-visualization-with-krona/main", + "number_of_steps": 3, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "kraken2", + "taxonomy_krona_chart", + "krakentools_kreport2krona" + ], + "update_time": "2024-07-15", + "versions": 1 + }, + { + "create_time": "2024-10-26", + "creators": [ + "ABRomics None", + "Pierre Marin", + "Clea Siguret" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Structural variation detection", + "Nucleic acid feature detection", + "Protein feature detection", + "Genome assembly", + "Parsing", + "Sequence motif recognition", "Genome annotation", "Data handling", "Multilocus sequence typing", "Scaffolding" ], "edam_topic": [], - "id": "1050", + "id": "1050", + "keep": true, + "latest_version": 9, + "license": "GPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1050?version=9", + "name": "bacterial_genome_annotation/main", + "number_of_steps": 6, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "abromics", + "annotation", + "genomics", + "bacterial-genomics", + "fasta", + "genome-annotation" + ], + "tools": [ + "tooldistillator", + "tooldistillator_summarize", + "integron_finder", + "isescan", + "plasmidfinder", + "bakta" + ], + "update_time": "2024-10-26", + "versions": 9 + }, + { + "create_time": "2024-10-26", + "creators": [ + "ABRomics None", + "Pierre Marin", + "Clea Siguret" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Antimicrobial resistance prediction", + "Data handling", + "Parsing" + ], + "edam_topic": [], + "id": "1049", + "keep": true, + "latest_version": 7, + "license": "GPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1049?version=7", + "name": "amr_gene_detection/main", + "number_of_steps": 5, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [ + "abromics", + "amr", + "amr-detection", + "genomics", + "antibiotic-resistance", + "antimicrobial resistance", + "antimicrobial-resistance-genes", + "bacterial-genomics", + "fasta" + ], + "tools": [ + "abricate", + "tooldistillator", + "tooldistillator_summarize", + "amrfinderplus", + "staramr_search" + ], + "update_time": "2024-10-27", + "versions": 7 + }, + { + "create_time": "2024-06-07", + "creators": [ + "Peter van Heusden" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence analysis", + "Variant calling", + "Sequence alignment analysis", + "Antimicrobial resistance prediction", + "Sequence alignment", + "Phylogenetic tree visualisation", + "Taxonomic classification", + "Sequencing quality control", + "Validation", + "Local alignment", + "Sequence contamination filtering", + "Phylogenetic tree generation", + "Global alignment" + ], + "edam_topic": [ + "Genetic variation", + "Infectious disease", + "Microbiology", + "Public health and epidemiology", + "Sequence assembly" + ], + "id": "1035", + "keep": true, + "latest_version": 1, + "license": "AGPL-3.0-or-later", + "link": "https://workflowhub.eu/workflows/1035?version=1", + "name": "TB Variant Analysis v1.0", + "number_of_steps": 15, + "projects": [ + "SANBI Pathogen Bioinformatics" + ], + "source": "WorkflowHub", + "tags": [ + "pathogen", + "tuberculosis" + ], + "tools": [ + "tb_variant_filter", + "snippy", + "qualimap_bamqc", + "kraken2", + "tp_sed_tool", + "__FLATTEN__", + "bcftools_consensus", + "tbvcfreport", + "multiqc", + "fastp", + "EMBOSS: seqret84", + "tb_profiler_profile", + "mosdepth", + "tp_awk_tool" + ], + "update_time": "2024-06-12", + "versions": 1 + }, + { + "create_time": "2024-05-30", + "creators": [ + "Matthias Bernt" + ], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Variant calling", + "DNA barcoding" + ], + "edam_topic": [], + "id": "790", "keep": true, - "latest_version": 9, - "license": "GPL-3.0-or-later", - "link": "https://workflowhub.eu/workflows/1050?version=9", - "name": "bacterial_genome_annotation/main", - "number_of_steps": 6, + "latest_version": 2, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/790?version=2", + "name": "dada2/main", + "number_of_steps": 14, "projects": [ "Intergalactic Workflow Commission (IWC)" ], "source": "WorkflowHub", "tags": [ - "abromics", - "annotation", - "genomics", - "bacterial-genomics", - "fasta", - "genome-annotation" + "name:amplicon" ], "tools": [ - "tooldistillator", - "tooldistillator_summarize", - "integron_finder", - "isescan", - "plasmidfinder", - "bakta" + "dada2_plotQualityProfile", + "dada2_filterAndTrim", + "__APPLY_RULES__", + "dada2_mergePairs", + "dada2_seqCounts", + "dada2_learnErrors", + "dada2_dada", + "dada2_assignTaxonomyAddspecies", + "dada2_removeBimeraDenovo", + "__UNZIP_COLLECTION__", + "dada2_makeSequenceTable" ], - "update_time": "2024-10-26", - "versions": 9 + "update_time": "2024-06-02", + "versions": 2 }, { - "create_time": "2024-10-26", + "create_time": "2024-02-14", "creators": [ - "ABRomics None", - "Pierre Marin", - "Clea Siguret" + "Anthony Bretaudeau" ], "deprecated": false, "doi": null, "edam_operation": [ - "Antimicrobial resistance prediction", - "Data handling", - "Parsing" + "Genome visualisation" ], "edam_topic": [], - "id": "1049", + "id": "749", "keep": true, - "latest_version": 7, - "license": "GPL-3.0-or-later", - "link": "https://workflowhub.eu/workflows/1049?version=7", - "name": "amr_gene_detection/main", + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/749?version=1", + "name": "Refining Genome Annotations with Apollo (prokaryotes)", "number_of_steps": 5, "projects": [ - "Intergalactic Workflow Commission (IWC)" + "EuroScienceGateway" ], "source": "WorkflowHub", "tags": [ - "abromics", - "amr", - "amr-detection", - "genomics", - "antibiotic-resistance", - "antimicrobial resistance", - "antimicrobial-resistance-genes", - "bacterial-genomics", - "fasta" + "genome-annotation" ], "tools": [ - "abricate", - "tooldistillator", - "tooldistillator_summarize", - "amrfinderplus", - "staramr_search" + "list_organism", + "create_or_update", + "iframe", + "jbrowse", + "create_account" ], - "update_time": "2024-10-27", - "versions": 7 + "update_time": "2024-02-15", + "versions": 1 }, { "create_time": "2023-10-26", @@ -1016,6 +1682,116 @@ "update_time": "2024-10-07", "versions": 1 }, + { + "create_time": "2024-08-12", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Visualisation", + "Aggregation" + ], + "edam_topic": [], + "id": "1349", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1349?version=1", + "name": "Calculating diversity from microbiome taxonomic data", + "number_of_steps": 6, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "name:gtn" + ], + "tools": [ + "krakentools_beta_diversity", + "krakentools_alpha_diversity" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-07-15", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence composition calculation", + "Statistical calculation", + "Sequence contamination filtering", + "Taxonomic classification", + "Cross-assembly", + "Expression analysis", + "Sequencing quality control" + ], + "edam_topic": [], + "id": "1344", + "keep": true, + "latest_version": 1, + "license": "GPL-3.0-or-later", + "link": "https://dev.workflowhub.eu/workflows/1344?version=1", + "name": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", + "number_of_steps": 6, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "sequence-analysis" + ], + "tools": [ + "recentrifuge", + "kraken2", + "fastqc", + "fastp", + "est_abundance" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-07-16", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Taxonomic classification", + "Cross-assembly", + "Statistical calculation", + "Expression analysis" + ], + "edam_topic": [], + "id": "1217", + "keep": true, + "latest_version": 2, + "license": "GPL-3.0-or-later", + "link": "https://dev.workflowhub.eu/workflows/1217?version=2", + "name": "Checking expected species and contamination in bacterial isolate", + "number_of_steps": 3, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "ecology" + ], + "tools": [ + "kraken2", + "recentrifuge", + "est_abundance" + ], + "update_time": "2024-10-07", + "versions": 2 + }, { "create_time": "2024-06-25", "creators": [], @@ -1565,6 +2341,48 @@ "update_time": "2024-10-07", "versions": 1 }, + { + "create_time": "2024-06-25", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence analysis", + "Sequence alignment analysis", + "Local alignment", + "Sequence alignment", + "Global alignment" + ], + "edam_topic": [], + "id": "1078", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://dev.workflowhub.eu/workflows/1078?version=1", + "name": "pox-virus-tiled-amplicon-ref-masking", + "number_of_steps": 14, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "variant-analysis" + ], + "tools": [ + "compose_text_param", + "Grep1", + "fasta_compute_length", + "EMBOSS: maskseq51", + "Cut1", + "Add_a_column1", + "param_value_from_file", + "datamash_ops" + ], + "update_time": "2024-10-07", + "versions": 1 + }, { "create_time": "2024-06-25", "creators": [], @@ -1616,6 +2434,63 @@ "update_time": "2024-10-07", "versions": 1 }, + { + "create_time": "2024-07-16", + "creators": [], + "deprecated": false, + "doi": null, + "edam_operation": [ + "Sequence analysis", + "Variant calling", + "Sequence alignment analysis", + "Antimicrobial resistance prediction", + "Sequence alignment", + "Phylogenetic tree visualisation", + "Taxonomic classification", + "Sequencing quality control", + "Validation", + "Local alignment", + "Sequence contamination filtering", + "Phylogenetic tree generation", + "Global alignment" + ], + "edam_topic": [], + "id": "1069", + "keep": true, + "latest_version": 2, + "license": "AGPL-3.0-or-later", + "link": "https://dev.workflowhub.eu/workflows/1069?version=2", + "name": "TB Variant Analysis v1.0", + "number_of_steps": 15, + "projects": [ + "Galaxy Training Network" + ], + "source": "dev.WorkflowHub", + "tags": [ + "gtn", + "galaxy", + "pathogen", + "tuberculosis" + ], + "tools": [ + "tb_variant_filter", + "snippy", + "qualimap_bamqc", + "kraken2", + "tp_sed_tool", + "__FLATTEN__", + "bcftools_consensus", + "tbvcfreport", + "multiqc", + "fastp", + "EMBOSS: seqret84", + "tb_profiler_profile", + "mosdepth", + "tp_awk_tool" + ], + "update_time": "2024-10-07", + "versions": 2 + }, { "create_time": "2024-06-25", "creators": [], diff --git a/communities/microgalaxy/resources/tag_filtered_workflows.tsv b/communities/microgalaxy/resources/tag_filtered_workflows.tsv index 63747011..db001083 100644 --- a/communities/microgalaxy/resources/tag_filtered_workflows.tsv +++ b/communities/microgalaxy/resources/tag_filtered_workflows.tsv @@ -1,8 +1,25 @@ Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +clinicalmp-discovery/main WorkflowHub 1225 https://workflowhub.eu/workflows/1225?version=1 Subina Mehta 2024-12-10 2025-01-13 1 1 24.0 tp_cat, Grep1, fasta2tab, dbbuilder, Remove beginning1, maxquant, Filter1, Cut1, msconvert, query_tabular, fasta_cli, fasta_merge_files_and_filter_unique_sequences, search_gui, Grouping1, ident_params, filter_tabular, peptide_shaker Protein quantification, Filtering, Imputation, Visualisation, Principal component plotting, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation, Formatting CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-data-interpretation/main WorkflowHub 1219 https://workflowhub.eu/workflows/1219?version=1 GalaxyP 2024-11-26 2024-12-06 1 1 6.0 msstatstmt, Grep1, unipept Visualisation, Prediction and recognition CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-verification/main WorkflowHub 1218 https://workflowhub.eu/workflows/1218?version=1 Pratik Jagtap 2024-11-26 2024-12-06 1 1 19.0 tp_cat, Remove beginning1, dbbuilder, pepquery2, Filter1, Cut1, query_tabular, uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences, Grouping1, collapse_dataset CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-database-generation/main WorkflowHub 1216 https://workflowhub.eu/workflows/1216?version=1 Subina Mehta 2024-11-23 2024-12-06 1 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences de Novo sequencing, Tag-based peptide identification, Protein identification, Target-Decoy, Expression analysis CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-quantitation/main WorkflowHub 1177 https://workflowhub.eu/workflows/1177?version=1 GalaxyP 2024-10-07 2024-10-07 1 1 7.0 "extracting microbial Peptides +Grep1, extract peptides +Cut1, maxquant, extract proteins +Cut1, extracting microbial Proteins +Grep1, Quantified-Peptides +Grouping1, Quantified-Proteins +Grouping1" Protein quantification, Imputation, Visualisation, Principal component plotting, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=7 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2024-11-26 2024-11-26 7 7 7.0 tooldistillator, bandage_info, tooldistillator_summarize, shovill, quast, refseq_masher_matches, bandage_image Sequence assembly visualisation, Data handling, Genome assembly, Parsing, Sequence assembly validation, Visualisation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=8 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2024-11-23 2024-11-23 8 8 6.0 recentrifuge, tooldistillator, tooldistillator_summarize, kraken2, fastp, est_abundance Data handling, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Parsing, Cross-assembly, Expression analysis, Sequencing quality control GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub 1090 https://workflowhub.eu/workflows/1090?version=2 Debjyoti Ghosh 2024-11-26 2024-12-06 2 2 3.0 Rarefaction, Taxonomic analysis, Phylogenetic tree for diversity analysis MIT Intergalactic Workflow Commission (IWC) True False +allele-based-pathogen-identification/main WorkflowHub 1063 https://workflowhub.eu/workflows/1063?version=3 Engy Nasr, Bérénice Batut, Paul Zierep 2024-10-30 2024-10-31 3 3 23.0 tp_head_tool, clair3, samtools_depth, snpSift_filter, regexColumn1, Remove beginning1, bcftools_norm, tp_cut_tool, table_compute, bcftools_consensus, samtools_coverage, minimap2, Count1, Cut1, Paste1, CONVERTER_gz_to_uncompressed, snpSift_extractFields, collapse_dataset Variant calling, Pairwise sequence alignment MIT Intergalactic Workflow Commission (IWC) True False +gene-based-pathogen-identification/main WorkflowHub 1062 https://workflowhub.eu/workflows/1062?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 1 1 15.0 __BUILD_LIST__, flye, abricate, compose_text_param, tp_find_and_replace, tab2fasta, param_value_from_file, collection_element_identifiers, medaka_consensus_pipeline, bandage_image, fasta2tab, split_file_to_collection Antimicrobial resistance prediction, Sequence assembly, Variant calling, Sequence assembly visualisation, Base-calling, Genome assembly, Cross-assembly, De-novo assembly, Mapping assembly MIT 10.48546/workflowhub.workflow.1062.1 Intergalactic Workflow Commission (IWC) True False +pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub 1060 https://workflowhub.eu/workflows/1060?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 1 1 60.0 tp_replace_in_column, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, clustalw, tab2fasta, Cut1, collapse_dataset, __FILTER_FAILED_DATASETS__, Remove beginning1, Count1, bedtools_getfastabed, Grouping1, regex1, regexColumn1, tp_split_on_column, fasttree, ggplot2_heatmap, newick_display, fasta2tab, collection_column_join, fasta_merge_files_and_filter_unique_sequences, tp_multijoin_tool Phylogenetic tree analysis, Phylogenetic tree generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree reconstruction, Visualisation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Mapping MIT 10.48546/workflowhub.workflow.1060.1 Intergalactic Workflow Commission (IWC) True False +taxonomy-profiling-and-visualization-with-krona/main WorkflowHub 1059 https://workflowhub.eu/workflows/1059?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2024-07-15 1 1 3.0 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT 10.48546/workflowhub.workflow.1059.1 Intergalactic Workflow Commission (IWC) True False bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2024-10-26 2024-10-26 9 9 6.0 tooldistillator, tooldistillator_summarize, integron_finder, isescan, plasmidfinder, bakta Structural variation detection, Nucleic acid feature detection, Protein feature detection, Genome assembly, Parsing, Sequence motif recognition, Genome annotation, Data handling, Multilocus sequence typing, Scaffolding GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=7 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2024-10-26 2024-10-27 7 7 5.0 abricate, tooldistillator, tooldistillator_summarize, amrfinderplus, staramr_search Antimicrobial resistance prediction, Data handling, Parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +dada2/main WorkflowHub 790 https://workflowhub.eu/workflows/790?version=2 Matthias Bernt name:amplicon 2024-05-30 2024-06-02 2 2 14.0 dada2_plotQualityProfile, dada2_filterAndTrim, __APPLY_RULES__, dada2_mergePairs, dada2_seqCounts, dada2_learnErrors, dada2_dada, dada2_assignTaxonomyAddspecies, dada2_removeBimeraDenovo, __UNZIP_COLLECTION__, dada2_makeSequenceTable Variant calling, DNA barcoding MIT Intergalactic Workflow Commission (IWC) True False pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=2 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2024-06-22 2024-06-22 2 2 40.0 " __FLATTEN__, __ZIP_COLLECTION__, datamash_ops, tp_cat, compose_text_param, @@ -12,6 +29,7 @@ pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?ver __APPLY_RULES__, EMBOSS: maskseq51, multiqc, ivar_trim, fastp, split_file_to_collection, samtools_stats, Grep1, samtools_merge, tp_sed_tool, collection_element_identifiers, __FILTER_FAILED_DATASETS__, bwa_mem" Sequence analysis, Sequence alignment analysis, Generation, Sequence alignment, Sequencing quality control, Read mapping, Validation, Local alignment, Sequence contamination filtering, Genome indexing, Global alignment MIT Intergalactic Workflow Commission (IWC) True False +Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub 749 https://workflowhub.eu/workflows/749?version=1 Anthony Bretaudeau genome-annotation 2024-02-14 2024-02-15 1 1 5.0 list_organism, create_or_update, iframe, jbrowse, create_account Genome visualisation CC-BY-4.0 EuroScienceGateway True False GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2023-02-13 1 1 12.0 PlasFlow, miniasm, unicycler, gfa_to_fa, minimap2, racon, nanoplot, bandage_image, staramr_search Sequence analysis, Scatter plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Genome assembly, Aggregation, De-novo assembly, Box-Whisker plot plotting, Mapping assembly Microbiology CC-BY-4.0 Galaxy Training Network True False 3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2023-02-13 1 1 2.0 fastp, shovill Sequence contamination filtering, Genome assembly, Sequencing quality control Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False 2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2023-02-13 1 1 7.0 ncbi_blastn_wrapper, shovill, minimap2, ngsutils_bam_filter, samtools_stats, fasta_merge_files_and_filter_unique_sequences, picard_SamToFastq Variant calling, Pairwise sequence alignment, Sequence contamination filtering, Read pre-processing, Genome assembly, Formatting, Sequencing quality control Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False @@ -30,10 +48,17 @@ Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 2.0 mothur_classify_seqs, mothur_remove_lineage Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 QCIF Bioinformatics True False Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_summary_seqs, mothur_screen_seqs, mothur_unique_seqs, mothur_count_seqs Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 QCIF Bioinformatics True False Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 9.0 mothur_screen_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_remove_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_pre_cluster Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 QCIF Bioinformatics True False +TB Variant Analysis v1.0 WorkflowHub 1035 https://workflowhub.eu/workflows/1035?version=1 Peter van Heusden pathogen, tuberculosis 2024-06-07 2024-06-12 1 1 15.0 tb_variant_filter, snippy, qualimap_bamqc, kraken2, tp_sed_tool, __FLATTEN__, bcftools_consensus, tbvcfreport, multiqc, fastp, EMBOSS: seqret84, tb_profiler_profile, mosdepth, tp_awk_tool Sequence analysis, Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence alignment, Phylogenetic tree visualisation, Taxonomic classification, Sequencing quality control, Validation, Local alignment, Sequence contamination filtering, Phylogenetic tree generation, Global alignment Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later SANBI Pathogen Bioinformatics True False +Workflow 3: AMR - SeqSero2/SISTR WorkflowHub 407 https://workflowhub.eu/workflows/407?version=1 bioinformatics, antimicrobial resistance 2022-11-24 2024-09-09 1 1 14.0 bbtools_tadpole, shovill, bbtools_bbduk, seqsero2, hamronize_tool, hamronize_summarize, __UNZIP_COLLECTION__, sistr_cmd, kma_map, mob_recon, srst2 Antimicrobial resistance prediction, RNA-Seq analysis, Sequence alignment, Genome assembly, Visualisation, Parsing, Sequence trimming, Read mapping, Genome alignment, Read binning, Data handling, Sequence contamination filtering, Genome indexing, Multilocus sequence typing GPL-3.0 Seq4AMR True False +Workflow 2: Sciensano WorkflowHub 644 https://workflowhub.eu/workflows/644?version=1 2023-11-07 2024-09-09 1 1 1.0 pipeline_stec_1.0 CC-BY-4.0 Seq4AMR True False Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2024-09-09 1 1 10.0 abricate, tp_find_and_replace, shovill, hamronize_tool, hamronize_summarize, collapse_dataset, staramr_search Antimicrobial resistance prediction, Data handling, Genome assembly, Parsing GPL-3.0 Seq4AMR True False +Workflow 1: AbritAMR WorkflowHub 634 https://workflowhub.eu/workflows/634?version=1 2023-10-31 2024-09-09 1 1 1.0 abritamr Antimicrobial resistance prediction CC-BY-4.0 Seq4AMR True False AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2024-12-24 2 2 36.0 , cat1, __APPLY_RULES__, Cut1, tp_text_file_with_recurring_lines, datamash_ops, collapse_dataset, Grep1, tp_find_and_replace, addValue, __MERGE_COLLECTION__, staramr_search, tp_split_on_column, shovill, hamronize_summarize, cat_multi_datasets, abricate, cast, hamronize_tool Antimicrobial resistance prediction, Data handling, Genome assembly, Parsing MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False Query a metaplasmidome database to identify and annotate plasmids in metagenomes dev.WorkflowHub 1380 https://dev.workflowhub.eu/workflows/1380?version=1 gtn, galaxy, metaplasmidome, name:microgalaxy, metagenomics 2025-01-13 2025-01-20 1 1 47.0 MQoutputfilter, join1, tp_replace_in_column, ggplot2_histogram, cat1, sort1, tp_sorted_uniq, CONVERTER_fasta_to_tabular, minimap2, count_gff_features, Filter1, tab2fasta, Cut1, Add_a_column1, tp_tail_tool, add_column_headers, Grouping1, histogram_rpy Visualisation, Pairwise sequence alignment MIT Galaxy Training Network True False Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' dev.WorkflowHub 1366 https://dev.workflowhub.eu/workflows/1366?version=1 fungi, gtn, galaxy, lotus2, ecology, metagenomics 2024-10-07 2024-10-07 1 1 1.0 lotus2 Sequence feature detection, DNA barcoding MIT Galaxy Training Network True False +Calculating diversity from microbiome taxonomic data dev.WorkflowHub 1349 https://dev.workflowhub.eu/workflows/1349?version=1 gtn, galaxy, name:gtn 2024-08-12 2024-10-07 1 1 6.0 krakentools_beta_diversity, krakentools_alpha_diversity Visualisation, Aggregation MIT Galaxy Training Network True False +Quality and contamination control in bacterial isolate using Illumina MiSeq Data dev.WorkflowHub 1344 https://dev.workflowhub.eu/workflows/1344?version=1 gtn, galaxy, sequence-analysis 2024-07-15 2024-10-07 1 1 6.0 recentrifuge, kraken2, fastqc, fastp, est_abundance Sequence composition calculation, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Cross-assembly, Expression analysis, Sequencing quality control GPL-3.0-or-later Galaxy Training Network True False +Checking expected species and contamination in bacterial isolate dev.WorkflowHub 1217 https://dev.workflowhub.eu/workflows/1217?version=2 gtn, galaxy, ecology 2024-07-16 2024-10-07 2 2 3.0 kraken2, recentrifuge, est_abundance Taxonomic classification, Cross-assembly, Statistical calculation, Expression analysis GPL-3.0-or-later Galaxy Training Network True False Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1133 https://dev.workflowhub.eu/workflows/1133?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 6.0 mothur_classify_otu, mothur_remove_groups, mothur_sub_sample, mothur_count_groups, mothur_make_shared, mothur_cluster_split Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1129 https://dev.workflowhub.eu/workflows/1129?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_rarefaction_single, mothur_summary_single, XY_Plot_1 Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1125 https://dev.workflowhub.eu/workflows/1125?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 4.0 mothur_dist_seqs, mothur_rarefaction_single, mothur_make_shared, mothur_cluster Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False @@ -46,7 +71,9 @@ Training: 16S rRNA Sequencing With Mothur: Main Tutorial dev.WorkflowHub 1101 ht Identification of the micro-organisms in a beer using Nanopore sequencing dev.WorkflowHub 1097 https://dev.workflowhub.eu/workflows/1097?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 8.0 porechop, kraken2, Filter1, fastqc, fastp, taxonomy_krona_chart, krakentools_kreport2krona Sequence composition calculation, Visualisation, Sequence contamination filtering, Taxonomic classification, Aggregation, Statistical calculation, Sequencing quality control MIT Galaxy Training Network True False Taxonomic Profiling and Visualization of Metagenomic Data dev.WorkflowHub 1095 https://dev.workflowhub.eu/workflows/1095?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 10.0 metaphlan, kraken2, interactive_tool_pavian, interactive_tool_phinch, est_abundance, __UNZIP_COLLECTION__, kraken_biom, taxonomy_krona_chart, krakentools_kreport2krona Phylogenetic tree analysis, Nucleic acid sequence analysis, Visualisation, Taxonomic classification, Aggregation, Statistical calculation MIT Galaxy Training Network True False Workflow 3: Functional Information (quick) dev.WorkflowHub 1080 https://dev.workflowhub.eu/workflows/1080?version=1 gtn, galaxy, asaim, metagenomics 2024-06-25 2024-10-07 1 1 12.0 humann_regroup_table, Grep1, humann_split_stratified_table, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_unpack_pathways, humann_rename_table, humann_renorm_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT Galaxy Training Network True False +pox-virus-tiled-amplicon-ref-masking dev.WorkflowHub 1078 https://dev.workflowhub.eu/workflows/1078?version=1 gtn, galaxy, variant-analysis 2024-06-25 2024-10-07 1 1 14.0 compose_text_param, Grep1, fasta_compute_length, EMBOSS: maskseq51, Cut1, Add_a_column1, param_value_from_file, datamash_ops Sequence analysis, Sequence alignment analysis, Local alignment, Sequence alignment, Global alignment MIT Galaxy Training Network True False Amplicon Tutorial dev.WorkflowHub 1070 https://dev.workflowhub.eu/workflows/1070?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 17.0 krona-text, mothur_screen_seqs, mothur_unique_seqs, mothur_classify_otu, mothur_filter_seqs, mothur_cluster_split, mothur_merge_files, mothur_make_biom, mothur_count_seqs, mothur_make_shared, mothur_make_group, mothur_summary_seqs, mothur_classify_seqs, mothur_align_seqs, mothur_pre_cluster Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding CC-BY-4.0 Galaxy Training Network True False +TB Variant Analysis v1.0 dev.WorkflowHub 1069 https://dev.workflowhub.eu/workflows/1069?version=2 gtn, galaxy, pathogen, tuberculosis 2024-07-16 2024-10-07 2 2 15.0 tb_variant_filter, snippy, qualimap_bamqc, kraken2, tp_sed_tool, __FLATTEN__, bcftools_consensus, tbvcfreport, multiqc, fastp, EMBOSS: seqret84, tb_profiler_profile, mosdepth, tp_awk_tool Sequence analysis, Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence alignment, Phylogenetic tree visualisation, Taxonomic classification, Sequencing quality control, Validation, Local alignment, Sequence contamination filtering, Phylogenetic tree generation, Global alignment AGPL-3.0-or-later Galaxy Training Network True False "WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" dev.WorkflowHub 1067 https://dev.workflowhub.eu/workflows/1067?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 7.0 metaphlan2, humann2, taxonomy_krona_chart, humann2_renorm_table, humann2_regroup_table, metaphlan2krona Visualisation CC-BY-4.0 Galaxy Training Network True False Training: 16S rRNA Analysis with Nanopore Sequencing Reads dev.WorkflowHub 1064 https://dev.workflowhub.eu/workflows/1064?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 11.0 datamash_reverse, porechop, Remove beginning1, kraken2, multiqc, fastqc, fastp, tp_replace_in_line, taxonomy_krona_chart Sequence composition calculation, Validation, Visualisation, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Sequencing quality control CC-BY-4.0 Galaxy Training Network True False Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1060 https://dev.workflowhub.eu/workflows/1060?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding MIT Galaxy Training Network True False diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py index d18e286c..9e683017 100644 --- a/sources/bin/extract_galaxy_workflows.py +++ b/sources/bin/extract_galaxy_workflows.py @@ -139,17 +139,32 @@ def add_projects(self, wf: dict) -> None: if "attributes" in wfhub_project["data"] and "title" in wfhub_project["data"]["attributes"]: self.projects.append(wfhub_project["data"]["attributes"]["title"]) - def test_tags(self, tags: dict) -> bool: + def get_source_tags(self, tags: dict) -> list: """ - Test if there are overlap between workflow tags and target tags + Get tags based on source """ if "WorkflowHub" in self.source: source = "workflowhub" else: source = "public" - matches = set(self.tags) & set(tags[source]) + return tags[source] + + def test_tags(self, tags: dict) -> bool: + """ + Test if there are overlap between workflow tags and target tags + """ + matches = set(self.tags) & set(self.get_source_tags(tags)) return len(matches) != 0 + def test_name(self, tags: dict) -> bool: + """ + Test if there are overlap between workflow tags and target tags + """ + for tag in self.get_source_tags(tags): + if tag in self.name: + return True + return False + def update_status(self, wf: dict) -> None: """ Update status from status table @@ -264,7 +279,7 @@ def filter_workflows_by_tags(self, tags: dict, status: Dict) -> None: for w in self.workflows: if w.link in status: w.update_status(status[w.link]) - if w.test_tags(tags): + if w.test_tags(tags) or w.test_name(tags): to_keep_wf.append(w) self.workflows = to_keep_wf