diff --git a/.github/workflows/fetch_filter_resources.yaml b/.github/workflows/fetch_filter_resources.yaml index ee30a248..b5aced85 100644 --- a/.github/workflows/fetch_filter_resources.yaml +++ b/.github/workflows/fetch_filter_resources.yaml @@ -101,6 +101,12 @@ jobs: - name: Generate wordcloud and interactive table run: | bash sources/bin/format_tools.sh + - name: Fetch all workflows + run: | + bash sources/bin/extract_all_workflows.sh + - name: Filter workflows for communities + run: | + bash sources/bin/get_community_workflows.sh - name: Fetch all tutorials run: | bash sources/bin/extract_all_tutorials.sh diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index fb4bcca0..1170c71c 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -6,14 +6,11 @@ concurrency: jobs: lint: runs-on: ubuntu-latest - strategy: - matrix: - python-version: ['3.8', '3.11'] steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: ${{ matrix.python-version }} + python-version: '3.11' - name: Install tox run: python -m pip install 'tox>=1.8.0' - name: Lint diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 28431a56..5ca93a36 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -1,16 +1,19 @@ name: Run tests -on: [push, pull_request_target] +on: [push, pull_request] jobs: test-tools: runs-on: ubuntu-20.04 + strategy: + matrix: + python-version: ['3.11'] environment: fetch-tools steps: - - name: Checkout main + - name: Checkout uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: ${{ matrix.python-version }} - name: Install requirement run: python -m pip install -r requirements.txt - name: Tool extraction @@ -26,12 +29,15 @@ jobs: bash sources/bin/format_tools.sh test-tutorials: runs-on: ubuntu-20.04 + strategy: + matrix: + python-version: ['3.11'] steps: - - name: Checkout main + - name: Checkout uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: ${{ matrix.python-version }} - name: Install requirement run: python -m pip install -r requirements.txt - name: Tutorial extraction @@ -41,4 +47,23 @@ jobs: PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }} - name: Tutorial filtering run: | - bash sources/bin/get_community_tutorials.sh test \ No newline at end of file + bash sources/bin/get_community_tutorials.sh test + test-workflows: + runs-on: ubuntu-20.04 + strategy: + matrix: + python-version: ['3.11'] + steps: + - name: Checkout + uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install requirement + run: python -m pip install -r requirements.txt + - name: Workflow extraction + run: | + bash sources/bin/extract_all_workflows.sh test + - name: Workflow filtering + run: | + bash sources/bin/get_community_workflows.sh test diff --git a/README.md b/README.md index 293f5b17..992a829f 100644 --- a/README.md +++ b/README.md @@ -6,4 +6,4 @@ Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools This repository stores the sources to build this catalog. The catalog is automatically updated every week. -Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN toturial**. +Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN tutorial**. diff --git a/communities/all/resources/test_workflows.json b/communities/all/resources/test_workflows.json new file mode 100644 index 00000000..5e18a8e9 --- /dev/null +++ b/communities/all/resources/test_workflows.json @@ -0,0 +1,56733 @@ +[ + { + "create_time": "2024-10-07", + "creators": [ + "Nadolina Brajuka" + ], + "doi": null, + "edam_operation": [ + "Taxonomic classification", + "Data handling" + ], + "edam_topic": [], + "id": "645", + "latest_version": 8, + "license": "BSD-3-Clause", + "link": "https://workflowhub.eu/workflows/645?version=8", + "name": "Assembly-decontamination-VGP9/main", + "number_of_steps": 10, + "source": "WorkflowHub", + "tags": [], + "tools": [ + "Cut1", + "tp_cat", + "Filter1", + "tp_sed_tool", + "ncbi_dustmasker_wrapper", + "parse_mito_blast", + "ncbi_blastn_wrapper", + "kraken2", + "gfastats" + ], + "update_time": "2024-10-13", + "versions": 8 + }, + { + "create_time": "2024-10-07", + "creators": [ + "VGP", + " Galaxy" + ], + "doi": null, + "edam_operation": [ + "Genome assembly", + "Sequence assembly validation", + "Scaffolding", + "Mapping", + "Transcriptome assembly", + "Sequence alignment", + "Visualisation", + "Data handling" + ], + "edam_topic": [], + "id": "625", + "latest_version": 12, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/625?version=12", + "name": "Scaffolding-HiC-VGP8/main", + "number_of_steps": 30, + "source": "WorkflowHub", + "tags": [], + "tools": [ + "", + "param_value_from_file", + "Cut1", + "bellerophon", + "ggplot2_point", + "bwa_mem2", + "pretext_snapshot", + "yahs", + "busco", + "__EXTRACT_DATASET__", + "bedtools_bamtobed", + "compose_text_param", + "tp_find_and_replace", + "gfastats", + "tp_sort_header_tool", + "pretext_map" + ], + "update_time": "2024-10-07", + "versions": 12 + }, + { + "create_time": "2024-10-07", + "creators": [ + "GalaxyP" + ], + "doi": null, + "edam_operation": [ + "Heat map generation", + "Statistical calculation", + "Visualisation", + "Protein quantification", + "Principal component plotting", + "Standardisation and normalisation", + "Imputation", + "Clustering" + ], + "edam_topic": [], + "id": "1177", + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/1177?version=1", + "name": "clinicalmp-quantitation/main", + "number_of_steps": 7, + "source": "WorkflowHub", + "tags": [], + "tools": [ + "extracting microbial Proteins\nGrep1", + "extract peptides\nCut1", + "extracting microbial Peptides\nGrep1", + "extract proteins\nCut1", + "Quantified-Proteins\nGrouping1", + "maxquant", + "Quantified-Peptides\nGrouping1" + ], + "update_time": "2024-10-07", + "versions": 1 + }, + { + "create_time": "2024-10-07", + "creators": [ + "Peter van Heusden" + ], + "doi": null, + "edam_operation": [ + "Tree-based sequence alignment", + "Generation", + "Variant calling", + "Methylation analysis", + "Genome indexing", + "Validation", + "Sequence alignment", + "Sequence contamination filtering", + "Variant classification", + "Sequencing quality control", + "SNP detection", + "Read mapping" + ], + "edam_topic": [], + "id": "155", + "latest_version": 5, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/155?version=5", + "name": "sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE", + "number_of_steps": 16, + "source": "WorkflowHub", + "tags": [], + "tools": [ + "pangolin", + "tp_cat", + "ivar_trim", + "__FLATTEN__", + "nextclade", + "qualimap_bamqc", + "ivar_consensus", + "tp_sed_tool", + "bwa_mem", + "samtools_view", + "multiqc", + "snpeff_sars_cov_2", + "samtools_stats", + "ivar_variants", + "fastp" + ], + "update_time": "2024-10-07", + "versions": 5 + }, + { + "create_time": "2024-10-07", + "creators": [ + "Wolfgang Maier" + ], + "doi": null, + "edam_operation": [], + "edam_topic": [], + "id": "109", + "latest_version": 9, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/109?version=9", + "name": "sars-cov-2-variation-reporting/COVID-19-VARIATION-REPORTING", + "number_of_steps": 30, + "source": "WorkflowHub", + "tags": [], + "tools": [ + "Cut1", + "tp_easyjoin_tool", + "Filter1", + 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abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-26 2024-09-26 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.eu ad8b6d73c9654305 https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-09-19 2024-09-19 1 1 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Taxonomic classification, Aggregation, Visualisation MIT +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.eu f6a763951d815944 https://usegalaxy.eu/published/workflow?id=f6a763951d815944 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-09-19 2024-09-19 1 1 clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, __FILTER_FAILED_DATASETS__ Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods) MIT +Nanopore Preprocessing (release v0.1) https://usegalaxy.eu 344cd3a3c2ce5302 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 Bérénice Batut, Engy Nasr, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:Nanopore, 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tooldistillator Parsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classification GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.0) https://usegalaxy.eu 3d937648809ca4e7 https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7 abromics-consortium, Abromics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-19 2024-09-19 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.1) https://usegalaxy.eu fca458178b3c794a https://usegalaxy.eu/published/workflow?id=fca458178b3c794a abromics-consortium, ABRomics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-19 2024-09-19 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.1.1) https://usegalaxy.eu 4216424f032c055f https://usegalaxy.eu/published/workflow?id=4216424f032c055f abromics-consortium, ABRomics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-19 2024-09-19 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +amr_gene_detection (release v1.0) https://usegalaxy.eu 41d207d06a32ba05 https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-19 2024-09-19 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +amr_gene_detection (release v1.1) https://usegalaxy.eu abe85758e77c78e6 https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-19 2024-09-19 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +amr_gene_detection (release v1.1.1) https://usegalaxy.eu f30f8e7dcd50cd0d https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-19 2024-09-19 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +dada2 amplicon analysis pipeline - for paired en (release v0.2) https://usegalaxy.eu 642f4c47028031d7 https://usegalaxy.eu/published/workflow?id=642f4c47028031d7 Matthias Bernt, UFZ Leipzig name:amplicon 2024-09-19 2024-09-19 1 1 dada2_dada, __APPLY_RULES__, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_seqCounts Variant calling, DNA barcoding MIT +Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.2) https://usegalaxy.eu 6e1fe7372e93fae0 https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0 Viktoria Isabel Schwarz, Wolfgang Maier pox, virology 2024-09-19 2024-09-19 1 1 ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51 Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignment MIT +LŠMB: Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 181e751be8dd9abc https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc Bérénice Batut, Teresa Müller, Polina Polunina Microbiome 2024-09-08 2024-09-08 0 0 taxonomy_krona_chart, Filter1, porechop, nanoplot, fastqc, kraken2, fastp, krakentools_kreport2krona Aggregation, Sequence composition calculation, Statistical calculation, Visualisation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plotting MIT +MGnify's amplicon pipeline v5.0 - Quality control SE https://usegalaxy.eu b7166aff73e5d81c https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c MGnify - EMBL, Rand Zoabi, Paul Zierep MGnify_Amplicon, amplicon, metagenomics 2024-03-25 2024-08-21 13 13 trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, prinseq, fastqc, tp_find_and_replace, fastq_filter Sequence composition calculation, Sequence trimming, Sequence contamination filtering, Sequencing quality control, Statistical calculation, Validation, Read pre-processing Apache-2.0 +MGnify's amplicon pipeline v5.0 - ITS https://usegalaxy.eu 169327ba670607d1 https://usegalaxy.eu/published/workflow?id=169327ba670607d1 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, amplicon, metagenomics 2024-05-06 2024-08-21 23 23 __FILTER_FROM_FILE__, taxonomy_krona_chart, tp_awk_tool, __FILTER_EMPTY_DATASETS__, collection_element_identifiers, biom_convert, mapseq, bedtools_maskfastabed Mapping, Formatting, Visualisation, k-mer counting Apache-2.0 +MGnify's amplicon pipeline v5.0 - Quality control PE https://usegalaxy.eu f9648091c06171cd https://usegalaxy.eu/published/workflow?id=f9648091c06171cd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, amplicon, metagenomics 2024-05-27 2024-08-21 14 14 __UNZIP_COLLECTION__, trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, fastq_filter, prinseq, mgnify_seqprep, fastqc, tp_find_and_replace, fastp Sequence composition calculation, Validation, Statistical calculation, Read pre-processing, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence trimming Apache-2.0 +MGnify's amplicon pipeline v5.0 - rRNA prediction https://usegalaxy.eu 0c3eee883f5ab977 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, metagenomics, amplicon 2024-05-06 2024-08-21 29 29 __FILTER_FROM_FILE__, taxonomy_krona_chart, tp_awk_tool, query_tabular, __FILTER_EMPTY_DATASETS__, cmsearch_deoverlap, collection_element_identifiers, gops_concat_1, cshl_fasta_formatter, biom_convert, infernal_cmsearch, bedtools_getfastabed, mapseq Formatting, Nucleic acid feature detection, k-mer counting, Alignment, Comparison, Mapping, Visualisation Apache-2.0 +MGnify's amplicon pipeline v5.0 - complete https://usegalaxy.eu 02f90a96d01fed4f https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, metagenomics, amplicon 2024-05-06 2024-08-21 79 79 fasterq_dump, __MERGE_COLLECTION__ Data handling Apache-2.0 +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microGalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-08-13 69 69 lotus2, taxonomy_krona_chart, ampvis2_load, __FLATTEN__, trimmomatic, collection_column_join, multiqc, ampvis2_ordinate, cutadapt, unzip, fastqc, kraken2, tp_cut_tool, krakentools_kreport2krona, ampvis2_heatmap Aggregation, Sequence composition calculation, Sequence trimming, Sequence feature detection, Validation, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Analysis, Sequencing quality control, Taxonomic classification, DNA barcoding MIT +Capripox isolate subtyping and consensus genome generation from WGS data https://usegalaxy.eu 629e57958afed44c https://usegalaxy.eu/published/workflow?id=629e57958afed44c Wolfgang Maier CaPV, VETLAB, virology 2024-07-28 2024-08-02 9 9 param_value_from_file, fasta_regex_finder, __FLATTEN__, qualimap_bamqc, ivar_consensus, __FILTER_FAILED_DATASETS__, bwa_mem, Show beginning1, read_it_and_keep, samtools_view, multiqc, tp_find_and_replace, fastp, collapse_dataset, __EXTRACT_DATASET__, vapor Generation, Data retrieval, Validation, Genome indexing, Sequence alignment, Filtering, Genome alignment, Sequence contamination filtering, Sequencing quality control, De-novo assembly, Read mapping AGPL-3.0-or-later +Pox Virus Illumina Amplicon Workflow from half-genomes https://usegalaxy.eu a31100610fba17a1 https://usegalaxy.eu/published/workflow?id=a31100610fba17a1 Viktoria Isabel Schwarz, Wolfgang Maier pox, virology 2024-08-02 2024-08-02 0 0 ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51 Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignment MIT +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microGalaxy, name:pallori, name:BloodRNA, name:UMI, name:Barcode, name:transcriptomics 2023-07-02 2024-07-29 37 37 umi_tools_extract, __FLATTEN__, featurecounts, __FILTER_FAILED_DATASETS__, collection_column_join, multiqc, fastqc, rna_star Validation, Sequence composition calculation, Statistical calculation, Sequencing quality control, Read summarisation, Sequence alignment, RNA-Seq quantification MIT +pAllori WGS https://usegalaxy.eu 4f245ac304ab76d9 https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 Engy Nasr, Paul Zierep name:pallori, name:microGalaxy, name:WGS 2024-07-16 2024-07-28 16 16 freebayes, Remove beginning1, ggplot2_heatmap, bowtie2, __FLATTEN__, vcf2tsv, tp_awk_tool, regexColumn1, abricate, trimmomatic, collection_column_join, multiqc, Grouping1, fastqc, snpSift_filter, shovill, bcftools_norm, bcftools_view Sequence composition calculation, Variant calling, Validation, Statistical calculation, Visualisation, Genome assembly, Antimicrobial resistance prediction, Sequencing quality control, Read mapping MIT +Influenza sequence data analysis https://usegalaxy.eu bc5ced57e711acf9 https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9 Wolfgang Maier, Viktoria Isabel Schwarz AIV, VETLAB, virology 2024-07-26 2024-07-28 21 21 map_param_value, iqtree, qualimap_bamqc, seqtk_subseq, bwa_mem, Show beginning1, __RELABEL_FROM_FILE__, snipit, collapse_dataset, Grep1, tp_find_and_replace, rbc_mafft, __EXTRACT_DATASET__, vapor, __APPLY_RULES__, ivar_consensus, __UNZIP_COLLECTION__, bamtools_split_ref, Paste1, __DUPLICATE_FILE_TO_COLLECTION__, pick_value, fastp, param_value_from_file, collection_element_identifiers, samtools_view, wc_gnu Generation, De-novo assembly, Data retrieval, Data handling, Phylogenetic analysis, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence file editing, Sequence contamination filtering, Sequencing quality control, Base position variability plotting, Sequence analysis, Read mapping, Multiple sequence alignment AGPL-3.0-or-later +MAGs workflow https://usegalaxy.eu 97312d273b6e8bd9 https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 name:microGalaxy 2023-11-15 2024-07-11 14 14 Fasta_to_Contig2Bin, samtools_sort, metabat2_jgi_summarize_bam_contig_depths, megahit, fastq_paired_end_interlacer, semibin, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_coverage_table, coverm_genome, bowtie2, __UNZIP_COLLECTION__, das_tool, metabat2, quast, checkm_lineage_wf, concoct_merge_cut_up_clustering, concoct, drep_dereplicate, maxbin2 Sequence clustering, Sequence composition calculation, Read binning, Sequence assembly validation, Sequence assembly, Statistical calculation, Validation, Visualisation, Genome comparison, Genome assembly, Local alignment, Sequencing quality control, Genome annotation, Read mapping +PathoGFAIR https://usegalaxy.eu 0dce37adb369492c https://usegalaxy.eu/published/workflow?id=0dce37adb369492c Engy Nasr, Bérénice Batut, Paul Zierep name:microGalaxy, name:IWC, name:PathoGFAIR, name:Nanopore, name:Collection 2024-05-31 2024-07-03 93 93 MIT +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.eu 376119528377a3ae https://usegalaxy.eu/published/workflow?id=376119528377a3ae Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-04-03 2024-06-24 58 58 clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, __FILTER_FAILED_DATASETS__ Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods) MIT +Allele-based Pathogen Identification https://usegalaxy.eu 09c7069ae409c362 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2023-04-12 2024-06-24 72 72 Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depth Variant calling, Pairwise sequence alignment MIT +Nanopore Preprocessing https://usegalaxy.eu a705370bc2c13d5c https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c Bérénice Batut, Engy Nasr, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:Nanopore, name:IWC 2023-04-12 2024-06-24 190 190 Cut1, samtools_fastx, krakentools_extract_kraken_reads, regexColumn1, __FILTER_FAILED_DATASETS__, Grep1, collection_column_join, multiqc, porechop, nanoplot, Add_a_column1, fastqc, kraken2, fastp, collapse_dataset, minimap2, bamtools_split_mapped Aggregation, Sequence composition calculation, Data handling, Validation, Statistical calculation, Visualisation, Sequence alignment analysis, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Pairwise sequence alignment, Taxonomic classification, Scatter plot plotting MIT +Taxonomy Profiling and Visualization with Phinch https://usegalaxy.eu b67b5ecd3305f830 https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microGalaxy, name:GTN 2023-04-12 2024-06-19 8 8 kraken2, interactive_tool_phinch, kraken_biom Taxonomic classification MIT +metaQuantome_datacreation_workflow https://usegalaxy.eu fc42cc9467c6ee8d https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics, name:microGalaxy 2023-12-14 2024-06-19 0 0 Cut1, Remove beginning1, flashlfq, regex1, query_tabular, Filter1, msconvert, tp_replace_in_line, tp_replace_in_column, search_gui, peptide_shaker, unipept Filtering, Prediction and recognition, Label-free quantification, Formatting, Visualisation +QIIME2 I: Demultiplexing (single-end) https://usegalaxy.eu 86b31ac8a7720e41 https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41 Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ name:amplicon, name:16S, name:tutorial 2024-06-12 2024-06-18 1 1 qiime2_core__tools__import, qiime2__demux__summarize, qiime2__demux__emp_single MIT +QIIME2 II: Denoising (sequence quality control) and feature table creation (single-end) https://usegalaxy.eu da17a4d690eb0ff3 https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3 Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ name:amplicon, name:16S, name:tutorial 2024-06-12 2024-06-18 1 1 qiime2__feature_table__tabulate_seqs, qiime2__feature_table__summarize, qiime2__metadata__tabulate, qiime2__dada2__denoise_single MIT +Gene-based Pathogen Identification https://usegalaxy.eu 585c21b7b1d864fc https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:PathoGFAIR, name:IWC, name:microGalaxy 2023-04-13 2024-06-05 142 142 param_value_from_file, bandage_image, medaka_consensus_pipeline, collection_element_identifiers, abricate, split_file_to_collection, tab2fasta, compose_text_param, tp_find_and_replace, __BUILD_LIST__, flye, fasta2tab Mapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assembly MIT +Taxonomy Profiling and Visualization with Krona https://usegalaxy.eu 10101558b211a782 https://usegalaxy.eu/published/workflow?id=10101558b211a782 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2023-05-11 2024-06-05 58 58 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Taxonomic classification, Aggregation, Visualisation MIT +FASTQC-MULTIQC-Quality-Check_FastQ_Files https://usegalaxy.eu 0ec684b341ad172d https://usegalaxy.eu/published/workflow?id=0ec684b341ad172d BGGM, Microbiome, Amplicon, FASTQC, QualityCheck 2024-05-13 2024-05-17 8 8 multiqc, fastqc Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation +Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool https://usegalaxy.eu c8bc4af6dd3b5d02 https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 Engy Nasr, Bérénice Batut microbiome, nanopore, IWC, name:Collection, name:microGalaxy 2022-11-29 2024-04-04 205 205 clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, interactive_tool_jupyter_notebook, __FILTER_FAILED_DATASETS__ Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods) MIT +Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microGalaxy 2023-10-10 2024-03-15 128 128 __BUILD_LIST__, interactive_tool_jupyter_notebook +dada2 amplicon analysis pipeline - for paired en (release v0.1) https://usegalaxy.eu b483cf6a138d2372 https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372 Matthias Bernt, UFZ Leipzig name:amplicon 2024-03-14 2024-03-14 1 1 dada2_dada, __APPLY_RULES__, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_seqCounts Variant calling, DNA barcoding MIT +Normalization https://usegalaxy.eu 0603f0898211f806 https://usegalaxy.eu/published/workflow?id=0603f0898211f806 name:microGalaxy 2023-09-25 2024-03-13 80 80 map_param_value, __FILTER_EMPTY_DATASETS__, Grep1, __BUILD_LIST__, __EXTRACT_DATASET__ +WF1_Database_Generation_Workflow https://usegalaxy.eu 7cfbf4b7bd3f30d3 https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 name:clinicalMP, name:microGalaxy 2023-12-14 2023-12-14 1 1 metanovo, fasta_merge_files_and_filter_unique_sequences Tag-based peptide identification, Target-Decoy, de Novo sequencing, Protein identification, Expression analysis +WF2_Discovery-Workflow https://usegalaxy.eu 8af41219411062ad https://usegalaxy.eu/published/workflow?id=8af41219411062ad name:microGalaxy, name:clinicalMP 2023-12-14 2023-12-14 1 1 Cut1, dbbuilder, Remove beginning1, tp_cat, query_tabular, Filter1, peptide_shaker, msconvert, Grep1, Grouping1, filter_tabular, maxquant, ident_params, search_gui, fasta_cli, fasta_merge_files_and_filter_unique_sequences, fasta2tab Heat map generation, Statistical calculation, Visualisation, Protein quantification, Filtering, Principal component plotting, Formatting, Standardisation and normalisation, Imputation, Clustering +WF3_VERIFICATION_WORKFLOW https://usegalaxy.eu d87fc6685e47d27d https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d name:microGalaxy, name:clinicalMP 2023-12-14 2023-12-14 1 1 Cut1, dbbuilder, Remove beginning1, tp_cat, pepquery2, query_tabular, Filter1, Grouping1, uniprotxml_downloader, collapse_dataset, fasta_merge_files_and_filter_unique_sequences +WF4_Quantitation_Workflow https://usegalaxy.eu a49275eb8b2b2ecb https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb name:clinicalMP, name:microGalaxy 2023-12-14 2023-12-14 1 1 Cut1, maxquant, Grep1, Grouping1 Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering +WF5_Data_Interpretation_Worklow https://usegalaxy.eu 755ede37d94dc456 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 name:microGalaxy, name:clinicalMP 2023-12-14 2023-12-14 1 1 Grep1, msstatstmt, unipept Prediction and recognition, Visualisation +MetaG_extended https://usegalaxy.eu d57d41e306241396 https://usegalaxy.eu/published/workflow?id=d57d41e306241396 name:microgalaxy 2023-12-14 2023-12-14 1 1 coverm_genome, tp_cat, fraggenescan, fasplit, tp_awk_tool, kofamscan, hmmer_hmmscan, tp_grep_tool, quast, interproscan, trim_galore, fastqc, sort1, maxbin2, cat_bins, coverm_contig, checkm_lineage_wf Data retrieval, Sequence assembly, Sequence generation, Visualisation, Protein feature detection, Local alignment, Conversion, Sequencing quality control, Format validation, Coding region prediction, Database search, Taxonomic classification, Sequence analysis, Sequence motif recognition, Sequence trimming, Multiple sequence alignment, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequence database search, Read pre-processing, Primer removal, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene functional annotation, Gene prediction +MetaP https://usegalaxy.eu 01ac8bf9832789e2 https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2 name:microgalaxy 2023-12-14 2023-12-14 1 1 maxquant Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering +MetaT https://usegalaxy.eu 3733bcdf5b458be7 https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7 name:microgalaxy 2023-12-14 2023-12-14 1 1 kallisto_quant, __UNZIP_COLLECTION__, collection_column_join, bg_sortmerna, trim_galore, fastqc Sequence composition calculation, Sequence similarity search, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming, Gene expression profiling +metaquantome-taxonomy-workflow https://usegalaxy.eu 695f7defb516d80d https://usegalaxy.eu/published/workflow?id=695f7defb516d80d proteomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 metaquantome_db, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_filter, metaquantome_stat Query and retrieval, Functional clustering, Heat map generation, Differential protein expression analysis, Indexing, Visualisation, Principal component visualisation, Filtering, Statistical inference, Quantification +metaquantome-function-worklow https://usegalaxy.eu 4c364c6be27981ba https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba proteomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 metaquantome_db, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_filter, metaquantome_stat Query and retrieval, Functional clustering, Heat map generation, Differential protein expression analysis, Indexing, Visualisation, Principal component visualisation, Filtering, Statistical inference, Quantification +Metaproteomics_GTN https://usegalaxy.eu 68967c922de149ae https://usegalaxy.eu/published/workflow?id=68967c922de149ae proteomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 query_tabular, sqlite_to_tabular, search_gui, peptide_shaker, unipept Prediction and recognition, Visualisation +Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_grep_tool, collapse_dataset, lastz_wrapper_2, join1, mergeCols1, bedtools_complementbed, tp_sed_tool, Grep1, bedtools_intersectbed, random_lines1, cat1, Filter1, datamash_ops, Cut1, tp_cat, fasta_compute_length, bedtools_sortbed, addValue, tp_sort_header_tool, fasta_filter_by_length Mapping, Read mapping, Sequence alignment +Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 08eb5e55109c4d9c https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, Remove beginning1, tp_replace_in_line, multiqc, porechop, fastqc, kraken2, fastp, datamash_reverse Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Validation, Visualisation, Statistical calculation +Main Metatranscriptomics Analysis https://usegalaxy.eu 7a08ecdf23e0c7a3 https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep name:microGalaxy 2023-12-14 2023-12-14 0 0 MIT +Copy Of GTN Training - Antibiotic Resistance Detection https://usegalaxy.eu 44e53ea319e07daa https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 bandage_image, staramr_search, gfa_to_fa, nanoplot, PlasFlow, miniasm, racon, unicycler, minimap2 Aggregation, Mapping assembly, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Sequence analysis, Scatter plot plotting, De-novo assembly +Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 0590554db9794d13 https://usegalaxy.eu/published/workflow?id=0590554db9794d13 Bérénice Batut, Teresa Müller, Polina Polunina Metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, Filter1, porechop, fastqc, kraken2, fastp, krakentools_kreport2krona Aggregation, Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Statistical calculation, Visualisation MIT +workflow-generate-dataset-for-assembly-tutorial https://usegalaxy.eu ce5c16ac23c4fbb1 https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_cat, bowtie2, seqtk_subseq, ngsutils_bam_filter, megahit, filter_tabular, bamtools, cutadapt, random_lines1, fastqc, bg_uniq Sequence composition calculation, Data handling, Variant calling, Statistical calculation, Read pre-processing, Sequence alignment analysis, Sequence file editing, Genome assembly, Formatting, Sequence contamination filtering, Primer removal, Sequencing quality control, Sequence trimming, Read mapping +Metagenomics assembly tutorial workflow https://usegalaxy.eu 62c47e3c9d4f3aa3 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 name:microGalaxy 2023-12-14 2023-12-14 0 0 bandage_image, bowtie2, collection_column_join, megahit, metaspades, quast, bandage_info, megahit_contig2fastg Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Read mapping, Visualisation +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" https://usegalaxy.eu c2b7ec5aacfc6107 https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, humann2_renorm_table, humann2, metaphlan2, humann2_regroup_table, metaphlan2krona Visualisation +Taxonomic Profiling and Visualization of Metagenomic Data https://usegalaxy.eu 4f0daf8e9dd54127 https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 Bérénice Batut Metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, __UNZIP_COLLECTION__, interactive_tool_pavian, interactive_tool_phinch, est_abundance, kraken2, metaphlan, krakentools_kreport2krona, kraken_biom Phylogenetic tree analysis, Aggregation, Nucleic acid sequence analysis, Taxonomic classification, Statistical calculation, Visualisation MIT +Amplicon Tutorial https://usegalaxy.eu 565c989730f68362 https://usegalaxy.eu/published/workflow?id=565c989730f68362 metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 mothur_make_group, mothur_make_biom, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_pre_cluster, krona-text, mothur_count_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_make_shared, mothur_summary_seqs, mothur_merge_files Sequence clustering, Phylogenetic analysis, Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding +Microbial Variant Calling https://usegalaxy.eu 515ef1601bc24a6c https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c variant-analysis, name:microGalaxy 2023-12-14 2023-12-14 0 0 snippy, jbrowse Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation +Calling variants in non-diploid systems https://usegalaxy.eu 291c36e1b18e9deb https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb variant-analysis, name:microGalaxy 2023-12-14 2023-12-14 0 0 freebayes, Cut1, picard_MergeSamFiles, vcf2tsv, picard_MarkDuplicates, bwa_mem, bamFilter, bamleftalign, fastqc, vcffilter2 Sequence composition calculation, Generation, Data handling, Variant calling, Statistical calculation, Genome indexing, Sequence alignment, Sequence alignment analysis, Formatting, Sequencing quality control, Read mapping +Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu c67d2e75eeb4fd19 https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_remove_groups, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_seq_error, mothur_tree_shared, mothur_cluster, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_get_groups, mothur_summary_single, newick_display, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearch Sequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding +Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microGalaxy 2023-12-14 2023-12-14 0 0 Cut1, cat1, Filter1, bg_diamond, regexColumn1, rapidnj, bg_diamond_view, rbc_mafft, gops_intersect_1, tp_split_on_column, Add_a_column1, tab2fasta, collapse_dataset, join1 Multiple sequence alignment, Phylogenetic tree generation, Sequence alignment analysis +Unicycler training https://usegalaxy.eu 8f3ce55d44d9f369 https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 assembly, name:microGalaxy 2023-12-14 2023-12-14 0 0 multiqc, prokka, quast, fastqc, unicycler Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Genome assembly, Sequencing quality control, Coding region prediction, Genome annotation, Gene prediction +Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microGalaxy 2023-12-14 2023-12-14 0 0 list_organism, create_account, create_or_update, jbrowse, iframe Genome visualisation +Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu e1894c36f1ab4ab4 https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 genome-annotation, name:microGalaxy 2023-12-14 2023-12-14 0 0 prokka, jbrowse Genome annotation, Coding region prediction, Genome visualisation, Gene prediction +Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_easyjoin_tool, regex1, tp_text_file_with_recurring_lines, gff2bed1, jbrowse, tbl2gff3, tab2fasta, tp_cut_tool, join1, bandage_image, staramr_search, Grep1, circos_interval_to_tile, PlasFlow, tp_split_on_column, bg_column_arrange_by_header, minimap2, medaka_consensus_pipeline, Filter1, tp_head_tool, trimmomatic, circos_wiggle_to_scatter, ncbi_blastn_wrapper, circos, Add_a_column1, flye, fasta2tab, fasta_compute_length, tp_cat, Cut1, circos_gc_skew, nanoplot, prokka, deeptools_bam_coverage, regex_replace, tp_sort_header_tool Sequence analysis, Variant calling, Mapping assembly, Sequence assembly, Gene prediction, Sequence visualisation, Cross-assembly, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Genome visualisation, Coding region prediction, Genome annotation, Base-calling, Scatter plot plotting, De-novo assembly +Mtb phylogeny https://usegalaxy.eu 875b3ca170ac12a1 https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 raxml, interactive_tool_rstudio Phylogenetic tree analysis, Sequence analysis +From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_cat, tb_variant_filter, bcftools_consensus, snp_dists, snp_sites +From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 __MERGE_COLLECTION__, tb_variant_filter, trimmomatic, snippy Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation +From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 tb_profiler_profile, tp_cat, addName, tp_sed_tool, tp_replace_in_line, samtools_view, tp_grep_tool, __MERGE_COLLECTION__ Antimicrobial resistance prediction +M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu 3ff4dbcc7a602e6b https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b Peter van Heusden variant-analysis, prokaryote, name:microGalaxy 2023-12-14 2023-12-14 0 0 tb_profiler_profile, tb_variant_filter, trimmomatic, multiqc, jbrowse, tbvcfreport, snippy, fastqc, kraken2 Sequence composition calculation, Phylogenetic tree generation, Variant calling, Validation, Phylogenetic tree visualisation, Statistical calculation, Antimicrobial resistance prediction, Sequencing quality control, Genome visualisation, Taxonomic classification MIT +Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microGalaxy, HPylori 2023-12-13 2023-12-13 2 2 freebayes, tp_awk_tool, bowtie2, vcf2tsv, snpSift_filter, bcftools_norm, bcftools_view Variant calling, Statistical calculation, Read mapping +Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microGalaxy, HPylori 2023-10-27 2023-12-13 13 13 freebayes, tp_cat, bowtie2, vcf2tsv, collection_element_identifiers, samtools_coverage, collapse_dataset, bcftools_norm, samtools_depth Variant calling, Statistical calculation, Read mapping +MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 437704898229dfb6 https://usegalaxy.eu/published/workflow?id=437704898229dfb6 MGnify_Amplicon_Showcase, name:microGalaxy 2023-12-12 2023-12-13 1 1 taxonomy_krona_chart, tp_awk_tool, query_tabular, cmsearch_deoverlap, gops_concat_1, biom_convert, infernal_cmsearch, bedtools_getfastabed, mapseq, bedtools_maskfastabed Formatting, Nucleic acid feature detection, k-mer counting, Alignment, Comparison, Mapping, Visualisation +MGnify amplicon QC https://usegalaxy.eu 8f415b0c409f56f7 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 MGnify_Amplicon_Showcase, name:microGalaxy 2023-12-13 2023-12-13 1 1 __UNZIP_COLLECTION__, trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, iuc_pear, prinseq, fastqc, tp_find_and_replace, fastp, fastq_dump Sequence composition calculation, Data handling, Validation, Sequence merging, Statistical calculation, Read pre-processing, Sequence contamination filtering, Sequencing quality control, Sequence trimming + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 4566262dd0acc8ab https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab metagenomics, metatranscriptomics, name:microGalaxy 2021-11-10 2023-12-07 2 2 featurecounts, bowtie2, multiqc Validation, Sequencing quality control, Read summarisation, Read mapping, RNA-Seq quantification +Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 9b9e1e28f3683f92 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 metagenomics, metatranscriptomics, name:microGalaxy 2021-11-01 2023-12-07 72 72 dbbuilder, translate_nucleotides, bowtie2, cat1, bg_diamond, cd_hit, kofamscan, metagene_annotator, bg_diamond_makedb, multiqc, megahit, bedtools_getfastabed, quast, fastqc, metaeuk_easy_predict, eggnog_mapper Sequence clustering, Information extraction, Query and retrieval, Homology-based gene prediction, Visualisation, Genome assembly, Sequencing quality control, Genome annotation, Mapping, Sequence analysis, Sequence composition calculation, Sequence assembly validation, Sequence annotation, Validation, Statistical calculation, Fold recognition, Gene functional annotation, Sequence alignment analysis, Read mapping +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu bb604ff5e010e7ab https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab metagenomics, metatranscriptomics, name:microGalaxy 2021-11-01 2023-12-07 51 51 trimmomatic, multiqc, fastqc Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu bdc7cfaac0db2eab https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab metagenomics, metatranscriptomics, name:microGalaxy 2022-06-29 2023-12-07 28 28 recentrifuge, bowtie2, seq_filter_by_id, filter_tabular, kraken2, fastq_to_tabular Taxonomic classification, Expression analysis, Read mapping, Cross-assembly +Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu e69b555faa6bb962 https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 metagenomics, metatranscriptomics, name:microGalaxy 2022-09-03 2023-12-07 18 18 recentrifuge, interactive_tool_phinch, kraken2, maaslin2, kraken_biom Filtering, Standardisation and normalisation, Taxonomic classification, Statistical calculation, Expression analysis, Visualisation, Cross-assembly +Main Metatranscriptomics Analysis 24.08.2023 https://usegalaxy.eu 81033ff723b9f22d https://usegalaxy.eu/published/workflow?id=81033ff723b9f22d microbiome 2023-08-24 2023-11-07 6 6 +pAllori ASiam Functional Information MT https://usegalaxy.eu a7a6d8ecc2795f58 https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microGalaxy, name:metatranscriptomics, name:AdaptedASiam, name:functionalProfiling 2023-07-07 2023-07-07 3 3 Cut1, humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, tp_find_and_replace, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT + pAllori ASiam Community Profile MT https://usegalaxy.eu 05f5f040337786bf https://usegalaxy.eu/published/workflow?id=05f5f040337786bf Engy Nasr, Bérénice Batut name:microGalaxy, name:metatranscriptomics, name:AdaptedASiam, name:communityProfiling 2023-06-30 2023-07-06 3 3 Cut1, taxonomy_krona_chart, graphlan, export2graphlan, graphlan_annotate, metaphlan Phylogenetic inference, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree editing MIT + pAllori ASiam Preprocessing MT https://usegalaxy.eu 72e3e5fdc766e24a https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microGalaxy, name:AdaptedASiam, name:metatranscriptomics, name:preprocessing 2023-06-30 2023-07-06 2 2 __FLATTEN__, multiqc, bg_sortmerna, fastq_paired_end_interlacer, cutadapt, fastqc Sequence composition calculation, Sequence similarity search, Validation, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming MIT +Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification https://usegalaxy.eu 3f0b104a74acf869 https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869 Engy Nasr, Bérénice Batut microbiome, nanopore 2023-01-16 2023-05-30 8 8 clair3, bcftools_consensus, bcftools_norm, snpSift_filter, minimap2, snpSift_extractFields Variant calling, Pairwise sequence alignment MIT +Pathogen-Detection-Nanopore-Gene-based-pathogenic-Identification https://usegalaxy.eu 2b888e200dfd91bc https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc Engy Nasr, Bérénice Batut microbiome, nanopore 2023-01-10 2023-05-30 20 20 mlst, bandage_image, Cut1, medaka_consensus_pipeline, cat1, add_line_to_file, abricate, tab2fasta, compose_text_param, tp_find_and_replace, tp_replace_in_column, flye, fasta2tab Mapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Multilocus sequence typing, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assembly MIT +Pathogen Detection-Nanopore-Taxonomy-Profiling-and-Visualization https://usegalaxy.eu a0ea6fc756dd17ea https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea Engy Nasr, Bérénice Batut microbiome, nanopore 2023-02-02 2023-05-30 4 4 kraken2, interactive_tool_phinch, kraken_biom Taxonomic classification MIT +Pathogen-Detection-Nanopore-Taxonomy-Profiling-and-Visualization-with-krona https://usegalaxy.eu ed2df13cfbc86b99 https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99 Engy Nasr, Bérénice Batut microbiome, nanopore 2023-02-17 2023-05-30 6 6 kraken2, krakentools_kreport2krona, krona-text Taxonomic classification, Aggregation, Visualisation MIT +Pathogen-Detection-Nanopore-Pre-Processing https://usegalaxy.eu 889f2782ad82bd69 https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69 Bérénice Batut, Engy Nasr microbiome, nanopore 2023-02-02 2023-05-30 6 6 porechop, nanoplot, multiqc, seq_filter_by_id, filter_tabular, fastqc, kraken2, fastp Sequence composition calculation, Validation, Statistical calculation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plotting MIT +Resistome workflow Pig Nov2021 (imported from uploaded file) https://usegalaxy.eu 25850714d13f0b0f https://usegalaxy.eu/published/workflow?id=25850714d13f0b0f Metagenomics, Resistome 2023-05-22 2023-05-23 0 0 bowtie2, resistome_analyzer, samtools_sort, bam_to_sam, rarefaction_analyzer, snpfinder, XY_Plot_1, fastp Sequencing quality control, Sequence contamination filtering, Read mapping +ASaiM-MT:metaphlan https://usegalaxy.eu ed0ad728cf21702b https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b ASaiM 2023-05-17 2023-05-17 3 3 taxonomy_krona_chart, metaphlan2, graphlan, format_metaphlan2_output, export2graphlan, graphlan_annotate, fastq_paired_end_interlacer, metaphlan2krona Phylogenetic inference, Phylogenetic tree visualisation, Visualisation, Formatting, Conversion, Taxonomic classification, Phylogenetic tree editing +Training: 16S rRNA RNIMU https://usegalaxy.eu dadca1020f586338 https://usegalaxy.eu/published/workflow?id=dadca1020f586338 metagenomics 2023-04-24 2023-04-27 8 8 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_tree_shared, mothur_chimera_vsearch, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_summary_single, newick_display, mothur_count_groups, mothur_make_shared, mothur_rarefaction_single Sequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding +MetaP https://usegalaxy.eu 96d198ed953449fd https://usegalaxy.eu/published/workflow?id=96d198ed953449fd name:microgalaxy 2020-01-30 2023-03-16 2 2 maxquant Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering +MetaG_extended https://usegalaxy.eu 6158c3b5fc12044e https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e name:microgalaxy 2023-02-10 2023-03-16 22 22 coverm_genome, tp_cat, fraggenescan, fasplit, tp_awk_tool, kofamscan, hmmer_hmmscan, tp_grep_tool, quast, interproscan, trim_galore, fastqc, sort1, maxbin2, cat_bins, coverm_contig, checkm_lineage_wf Data retrieval, Sequence assembly, Sequence generation, Visualisation, Protein feature detection, Local alignment, Conversion, Sequencing quality control, Format validation, Coding region prediction, Database search, Taxonomic classification, Sequence analysis, Sequence motif recognition, Sequence trimming, Multiple sequence alignment, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequence database search, Read pre-processing, Primer removal, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene functional annotation, Gene prediction +Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.1) https://usegalaxy.eu b77e3b08092fa73e https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e Viktoria Isabel Schwarz, Wolfgang Maier pox, virology 2023-03-02 2023-03-02 1 1 ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51 Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignment MIT +MetaT https://usegalaxy.eu 385cc7df70d7916b https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b name:microgalaxy 2020-01-27 2023-02-27 16 16 kallisto_quant, __UNZIP_COLLECTION__, collection_column_join, bg_sortmerna, trim_galore, fastqc Sequence composition calculation, Sequence similarity search, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming, Gene expression profiling +Nanopore Datasets - Pre-Processing https://usegalaxy.eu 57d3109f32defa3b https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b , , Bérénice Batut, , Engy Nasr microbiome, nanopore 2022-08-07 2023-01-29 71 71 porechop, nanoplot, multiqc, seq_filter_by_id, filter_tabular, fastqc, kraken2, fastp Sequence composition calculation, Validation, Statistical calculation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plotting MIT +Bacterial genome assembly - IZSPB https://usegalaxy.eu 37da7b42cb063a3a https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a assembly, bacterial, genome 2021-07-27 2022-12-03 18 18 mlst, spades, abricate, multiqc, prokka, quast, abricate_summary, fastp Sequence assembly validation, Validation, Visualisation, Genome assembly, Antimicrobial resistance prediction, Multilocus sequence typing, Sequence contamination filtering, Sequencing quality control, Coding region prediction, Genome annotation, Gene prediction +16S rDNA microbial analisys + MUSCLE mothur https://usegalaxy.eu 6d06bd22f206e176 https://usegalaxy.eu/published/workflow?id=6d06bd22f206e176 16S, mothur, microbial, microbiome, OTU, Cluster, Rarefaction 2021-08-09 2022-07-29 8 8 mothur_chimera_uchime, mothur_get_oturep, mothur_unique_seqs, mothur_rarefaction_single, mothur_dist_seqs, mothur_remove_seqs, muscle, mothur_cluster Sequence clustering, Phylogenetic analysis, Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding +Metatranscriptomics-WF3: Functional Information (quick) https://usegalaxy.eu 5ce8a472e6e95c60 https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60 metagenomics 2021-05-25 2021-11-09 8 8 humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis +Metatranscriptomics-WF3: Functional Information https://usegalaxy.eu 23dd2253da51e22e https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e metagenomics 2021-05-25 2021-11-09 6 6 humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis +Metatranscriptomics - analyze human RNA-seq data with Kraken (imported from uploaded file) https://usegalaxy.eu ee0005a5487653ba https://usegalaxy.eu/published/workflow?id=ee0005a5487653ba None metatranscriptomics, Kraken, RNA-seq, microbiome 2021-10-18 2021-10-18 2 2 taxonomy_krona_chart, Kraken2Tax, picard_SamToFastq, trimmomatic, samtools_view, bwa, fastqc, kraken2 Sequence composition calculation, Generation, Statistical calculation, Genome indexing, Sequence alignment, Visualisation, Formatting, Sequencing quality control, Taxonomic classification, Read mapping +Taxonomic and functional community profiling of raw metagenomic shotgun data workflow https://usegalaxy.eu a8f829deb69b30ab https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab asaim 2021-06-22 2021-06-24 14 14 taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, fastq_paired_end_interlacer, cutadapt, humann_unpack_pathways, Grep1, format_metaphlan2_output, graphlan_annotate, combine_metaphlan2_humann2, humann, bg_sortmerna, export2graphlan, humann_regroup_table, fastqc, Cut1, humann2_genefamilies_genus_level, graphlan, multiqc, humann_renorm_table, metaphlan, humann_rename_table Sequence similarity search, Phylogenetic analysis, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Sequencing quality control, Taxonomic classification, Sequence trimming, Phylogenetic tree editing, Sequence composition calculation, Phylogenetic inference, Statistical calculation, Validation, Read pre-processing, Primer removal, Sequence alignment analysis, Formatting, Nucleic acid sequence analysis, Species frequency estimation, Sequence comparison +Metatranscriptomcis-WF2: Community Profile https://usegalaxy.eu 19de5cbae7f48103 https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103 metagenomics 2021-05-25 2021-05-25 2 2 Cut1, taxonomy_krona_chart, graphlan, export2graphlan, graphlan_annotate, metaphlan Phylogenetic inference, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree editing +Metatranscriptomics-WF1: Preprocessing https://usegalaxy.eu f6e8a63283262518 https://usegalaxy.eu/published/workflow?id=f6e8a63283262518 metagenomics 2021-05-25 2021-05-25 2 2 bg_sortmerna, multiqc, fastq_paired_end_interlacer, cutadapt, fastqc Sequence composition calculation, Sequence similarity search, Validation, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming +ASaiM-MT https://usegalaxy.eu dfc2c53ac3103eff https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff ASaiM 2020-12-04 2020-12-04 1 1 taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, fastq_paired_end_interlacer, cutadapt, humann2, Grep1, format_metaphlan2_output, graphlan_annotate, Grouping1, humann2_unpack_pathways, metaphlan2krona, metaphlan2, combine_metaphlan2_humann2, bg_sortmerna, export2graphlan, fastqc, humann2_renorm_table, humann2_genefamilies_genus_level, graphlan, multiqc, tp_sort_header_tool Sequence similarity search, Phylogenetic tree visualisation, Visualisation, Conversion, Sequencing quality control, Taxonomic classification, Sequence trimming, Phylogenetic tree editing, Sequence composition calculation, Phylogenetic inference, Statistical calculation, Validation, Read pre-processing, Primer removal, Sequence alignment analysis, Formatting, Sequence comparison +Workflow 3: Functional Information [Metatranscriptomics] https://usegalaxy.eu c817aefc77933d79 https://usegalaxy.eu/published/workflow?id=c817aefc77933d79 metagenomics 2020-07-13 2020-07-14 1 1 humann2_renorm_table, humann2, humann2_unpack_pathways, group_humann2_uniref_abundances_to_go +0_Short-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) https://usegalaxy.eu 374797e58377c40f https://usegalaxy.eu/published/workflow?id=374797e58377c40f Assembly, Unicycler, StarAMR, Bacterial, Prokka, Short-Read, Illumina 2020-06-24 2020-06-24 4 4 bandage_image, staramr_search, multiqc, prokka, quast, bandage_info, fastqc, unicycler, fastp Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Genome assembly, Sequence contamination filtering, Sequencing quality control, Sequence assembly visualisation, Coding region prediction, Genome annotation, Gene prediction +0_Hybrid_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) https://usegalaxy.eu ecf48fa50af560a0 https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0 Hybrid, Assembly, ONT, Unicycler, StarAMR, Bacterial, Prokka 2020-06-24 2020-06-24 13 13 filtlong, bandage_image, Cut1, staramr_search, bedtools_genomecoveragebed, multiqc, nanoplot, prokka, quast, bandage_info, Summary_Statistics1, fastqc, unicycler, fastp, minimap2 Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Filtering, Genome assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Mapping, Pairwise sequence alignment, Scatter plot plotting, Gene prediction +0_Long-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) https://usegalaxy.eu ea485dbabc76488d https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d Assembly, ONT, Unicycler, StarAMR, Bacterial, Prokka, Coverage 2020-06-24 2020-06-24 3 3 filtlong, bandage_image, Cut1, staramr_search, bedtools_genomecoveragebed, nanoplot, prokka, quast, bandage_info, Summary_Statistics1, unicycler, minimap2 Aggregation, Sequence assembly validation, Visualisation, Filtering, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Mapping, Scatter plot plotting, Gene prediction +MetaGalaxy https://usegalaxy.eu 5826e573b6f93762 https://usegalaxy.eu/published/workflow?id=5826e573b6f93762 Long_Read, Metagenomics, Assembly, AMR, Taxonomy, Gene_Annotation, Long_Read 2020-01-22 2020-04-21 1 1 Cut1, filtlong, bandage_image, mlst, abricate, nanoplot, Krona, racon, prokka, jbrowse, quast, bandage_info, kraken2, meta_flye, minimap2 Sequence assembly validation, Mapping assembly, Visualisation, Taxonomic classification, Filtering, Genome assembly, Multilocus sequence typing, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Genome visualisation, Pairwise sequence alignment, Scatter plot plotting, Gene prediction +MetaGalaxy (4x polishing w Racon) https://usegalaxy.eu a337bfb2eb1e583f https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f Nanopore, Metagenomics, ONT 2020-01-31 2020-02-10 4 4 Cut1, filtlong, taxonomy_krona_chart, bandage_image, mlst, minimap2, abricate, nanoplot, racon, jbrowse, prokka, quast, bandage_info, kraken2, flye Mapping assembly, Visualisation, Cross-assembly, Genome assembly, Multilocus sequence typing, Pairwise sequence alignment, Sequencing quality control, Coding region prediction, Taxonomic classification, Genome annotation, De-novo assembly, Sequence assembly validation, Filtering, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Genome visualisation, Scatter plot plotting, Gene prediction +MetaGalaxy https://usegalaxy.eu a84bac86ec183d46 https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46 Nanopore, Metagenomics, ONT 2020-01-24 2020-02-10 8 8 Cut1, filtlong, taxonomy_krona_chart, bandage_image, mlst, minimap2, abricate, nanoplot, racon, jbrowse, prokka, quast, bandage_info, kraken2, flye Mapping assembly, Visualisation, Cross-assembly, Genome assembly, Multilocus sequence typing, Pairwise sequence alignment, Sequencing quality control, Coding region prediction, Taxonomic classification, Genome annotation, De-novo assembly, Sequence assembly validation, Filtering, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Genome visualisation, Scatter plot plotting, Gene prediction +16S microbial analysis (Mothur) https://usegalaxy.eu ce21961260fe4351 https://usegalaxy.eu/published/workflow?id=ce21961260fe4351 Metagenomics, Mothur, 16S 2018-09-22 2018-09-22 1 1 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_heatmap_bin, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, collapse_dataset, mothur_make_contigs, mothur_pcoa, mothur_classify_otu, mothur_get_oturep, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, fasttree, mothur_venn, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_summary_single, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearch Sequence clustering, Phylogenetic analysis, Phylogenetic tree generation (from molecular sequences), Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding, Phylogenetic tree generation (maximum likelihood and Bayesian methods) +ASaiM - Metagenomic assembly with MetaSPAdes https://usegalaxy.eu 579ff83177c5ee09 https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 ASaiM 2018-01-17 2018-08-03 3 3 bowtie2, valet, multiqc, metaspades, quast, trim_galore, fastqc Sequence composition calculation, Sequence assembly validation, Validation, Sequence assembly, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence trimming, Read mapping +ASaiM - Metagenomic assembly with MEGAHIT https://usegalaxy.eu 1524b189069b42a5 https://usegalaxy.eu/published/workflow?id=1524b189069b42a5 ASaiM 2018-01-17 2018-08-03 4 4 bowtie2, valet, multiqc, megahit, quast, trim_galore, fastqc Sequence composition calculation, Sequence assembly validation, Validation, Sequence assembly, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence trimming, Read mapping +ASaiM - Shotgun workflow for paired-end data collection https://usegalaxy.eu 329cf724a21f13ec https://usegalaxy.eu/published/workflow?id=329cf724a21f13ec ASaiM 2018-04-30 2018-04-30 1 1 +Shotgun workflow for paired-end data (imported from uploaded file) https://usegalaxy.eu 358db17bfc1ee330 https://usegalaxy.eu/published/workflow?id=358db17bfc1ee330 ASaiM 2018-01-29 2018-04-30 0 0 fastq_join +ASaiM - Shotgun workflow for single-end data collection https://usegalaxy.eu 1c3adfc77a138ef6 https://usegalaxy.eu/published/workflow?id=1c3adfc77a138ef6 ASaiM 2018-01-29 2018-04-30 2 2 +QIIME - Illumina Overview tutorial (imported from uploaded file) https://usegalaxy.eu 3acfb87be6db2303 https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303 ASaiM 2018-01-17 2018-01-17 0 0 qiime_pick_open_reference_otus, qiime_split_libraries_fastq, qiime_core_diversity, qiime_validate_mapping_file, qiime_count_seqs Phylogenetic analysis, Visualisation, Sequencing quality control, Taxonomic classification, Demultiplexing +EBI Metagenomics workflow (3.0) (imported from uploaded file) https://usegalaxy.eu 58955868b504c60d https://usegalaxy.eu/published/workflow?id=58955868b504c60d ASaiM 2018-01-17 2018-01-17 0 0 hmmer_hmmsearch, cshl_fastq_to_fasta, tp_awk_tool, tp_cat, fraggenescan, trimmomatic, seq_filter_by_id, hmmer_hmmbuild, interproscan, qiime_pick_closed_reference_otus Data retrieval, Phylogenetic analysis, Sequence generation, Visualisation, Protein feature detection, Conversion, Sequencing quality control, Format validation, Database search, Taxonomic classification, Sequence motif recognition, Multiple sequence alignment, Demultiplexing, Statistical calculation, Sequence database search, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene prediction diff --git a/pyproject.toml b/pyproject.toml index ca4018da..32e1a463 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,10 +7,12 @@ include = '\.pyi?$' isort = true [tool.ruff] +target-version = "py38" + +[tool.ruff.lint] # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B), # flake8-logging-format (G) and pyupgrade (UP) select = ["E", "F", "B", "G", "UP"] -target-version = "py38" # Exceptions: # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body) # B9 flake8-bugbear opinionated warnings diff --git a/sources/README.md b/sources/README.md index 9a6128f2..52fd7657 100644 --- a/sources/README.md +++ b/sources/README.md @@ -240,6 +240,20 @@ To make a test run of the tool to check its functionalities follow [Usage](#Usag $ bash sources/bin/get_community_tutorials.sh test ``` +### Workflows + +1. Workflow extraction + + ```bash + $ bash bin/extract_all_workflows.sh test + ``` + +2. Workflow filtering + + ```bash + $ bash bin/get_community_workflowss.sh test + ``` + # Galaxy Labs framework ## What is a Galaxy Lab? diff --git a/sources/bin/extract_all_workflows.sh b/sources/bin/extract_all_workflows.sh new file mode 100644 index 00000000..c89e79b4 --- /dev/null +++ b/sources/bin/extract_all_workflows.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +if [ ! -z $1 ] +then + python sources/bin/extract_galaxy_workflows.py extract \ + --all communities/all/resources/test_workflows.json \ + --tools communities/all/resources/tools.json \ + --test +else + python sources/bin/extract_galaxy_workflows.py extract \ + --all communities/all/resources/workflows.json \ + --tools communities/all/resources/tools.json +fi \ No newline at end of file diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py new file mode 100644 index 00000000..4ff03f75 --- /dev/null +++ b/sources/bin/extract_galaxy_workflows.py @@ -0,0 +1,306 @@ +#!/usr/bin/env python + +import argparse +from typing import ( + Any, + Dict, + List, +) + +import pandas as pd +import shared + + +class Workflow: + """ + Class for workflow + """ + + def __init__(self) -> None: + self.source = "" + self.id = 0 + self.link = "" + self.name = "" + self.creators: List[str] = [] + self.tags: List[str] = [] + self.create_time = "" + self.update_time = "" + self.latest_version = 0 + self.versions = 0 + self.number_of_steps = 0 + self.tools: List[str] = [] + self.edam_operation: List[str] = [] + self.edam_topic: List[str] = [] + self.license = "" + self.doi = "" + + def init_by_importing(self, wf: dict) -> None: + self.source = wf["source"] + self.id = wf["id"] + self.link = wf["link"] + self.name = wf["name"] + self.creators = wf["creators"] + self.tags = wf["tags"] + self.create_time = wf["create_time"] + self.update_time = wf["update_time"] + self.latest_version = wf["latest_version"] + self.versions = wf["versions"] + self.number_of_steps = wf["number_of_steps"] + self.tools = wf["tools"] + self.edam_operation = wf["edam_operation"] + self.edam_topic = wf["edam_topic"] + self.license = wf["license"] + self.doi = wf["doi"] + + def init_from_search(self, wf: dict, source: str, tools: dict) -> None: + self.source = source + if self.source == "WorkflowHub": + self.id = wf["data"]["id"] + self.link = f"https://workflowhub.eu{ wf['data']['links']['self'] }" + self.name = wf["data"]["attributes"]["title"] + self.tags = wf["data"]["attributes"]["tags"] + self.create_time = shared.format_date(wf["data"]["attributes"]["created_at"]) + self.update_time = shared.format_date(wf["data"]["attributes"]["updated_at"]) + self.latest_version = wf["data"]["attributes"]["latest_version"] + self.versions = len(wf["data"]["attributes"]["versions"]) + self.number_of_steps = len(wf["data"]["attributes"]["internals"]["steps"]) + self.license = wf["data"]["attributes"]["license"] + self.doi = wf["data"]["attributes"]["doi"] + self.edam_topic = [t["label"] for t in wf["data"]["attributes"]["topic_annotations"]] + else: + self.id = wf["id"] + self.link = f"{ source }/published/workflow?id={ wf['id'] }" + self.name = wf["name"] + self.add_creators(wf) + self.number_of_steps = wf["number_of_steps"] if "number_of_steps" in wf else len(wf["steps"].keys()) + self.tags = wf["tags"] + self.create_time = shared.format_date(wf["create_time"]) + self.update_time = shared.format_date(wf["update_time"]) + self.latest_version = wf["version"] + self.versions = wf["version"] + self.license = wf["license"] + + self.add_creators(wf) + self.add_tools(wf) + self.edam_operation = shared.get_edam_operation_from_tools(self.tools, tools) + + def add_creators(self, wf: dict) -> None: + """ + Get workflow creators + """ + self.creators = [] + if self.source == "WorkflowHub": + creators = wf["data"]["attributes"]["creators"] + if len(creators) == 0: + other = wf["data"]["attributes"]["other_creators"] + if other and len(other) > 0: + self.creators.extend(wf["data"]["attributes"]["other_creators"].split(",")) + else: + self.creators.extend([f"{c['given_name']} {c['family_name']}" for c in creators]) + else: + if "creator" in wf and wf["creator"] is not None: + self.creators.extend([c["name"] for c in wf["creator"]]) + + def add_tools(self, wf: dict) -> None: + """ + Extract list of tool ids from workflow + """ + tools = set() + if self.source == "WorkflowHub": + for tool in wf["data"]["attributes"]["internals"]["steps"]: + if tool["description"] is not None: + tools.add(shared.shorten_tool_id(tool["description"])) + else: + for step in wf["steps"].values(): + if "tool_id" in step and step["tool_id"] is not None: + tools.add(shared.shorten_tool_id(step["tool_id"])) + self.tools = list(tools) + + +class Workflows: + """ + Class Workflows + """ + + def __init__(self, test: bool = False) -> None: + self.workflows: List[Workflow] = [] + self.tools: Dict[Any, Any] = {} + self.test = test + + def init_by_searching(self, tool_fp: str) -> None: + self.tools = shared.read_suite_per_tool_id(tool_fp) + self.add_workflows_from_workflowhub() + self.add_workflows_from_public_servers() + + def init_by_importing(self, wfs: dict) -> None: + for iwf in wfs: + wf = Workflow() + wf.init_by_importing(iwf) + self.workflows.append(wf) + + def add_workflows_from_workflowhub(self) -> None: + """ + Add workflows from WorkflowHub + """ + header = {"Accept": "application/json"} + wfhub_wfs = shared.get_request_json( + "https://workflowhub.eu/workflows?filter[workflow_type]=galaxy", + header, + ) + print(f"Workflows from WorkflowHub: {len(wfhub_wfs['data'])}") + data = wfhub_wfs["data"] + if self.test: + data = data[:10] + for wf in data: + wfhub_wf = shared.get_request_json( + f"https://workflowhub.eu{wf['links']['self']}", + header, + ) + wf = Workflow() + wf.init_from_search(wf=wfhub_wf, source="WorkflowHub", tools=self.tools) + self.workflows.append(wf) + print(len(self.workflows)) + + def add_workflows_from_a_server(self, server: str) -> None: + """ + Extract public workflows from a server + """ + header = {"Accept": "application/json"} + server_wfs = shared.get_request_json( + f"{server}/api/workflows/", + header, + ) + count = 0 + for wf in server_wfs: + if wf["published"] and wf["importable"] and not wf["deleted"] and not wf["hidden"]: + count += 1 + server_wf = shared.get_request_json( + f"{server}/api/workflows/{wf['id']}", + header, + ) + wf = Workflow() + wf.init_from_search(wf=server_wf, source=server, tools=self.tools) + self.workflows.append(wf) + print(f"Workflows from {server}: {count}") + + def add_workflows_from_public_servers(self) -> None: + """ + Extract workflows from UseGalaxy servers + """ + server_urls = [ + "https://usegalaxy.fr", + "https://usegalaxy.cz", + "https://usegalaxy.eu", + "https://usegalaxy.org", + "https://usegalaxy.org.au", + ] + if self.test: + server_urls = server_urls[2:3] + for url in server_urls: + print(url) + self.add_workflows_from_a_server(url) + + def export_workflows_to_dict(self) -> List: + """ + Export workflows as dictionary + """ + return [w.__dict__ for w in self.workflows] + + def filter_workflows_by_tags(self, tags: list) -> None: + """ + Filter workflows by tags + """ + to_keep_wf = [] + for w in self.workflows: + wf_tags = [w.lower() for w in w.tags] + matches = set(wf_tags) & set(tags) + if len(matches) != 0: + to_keep_wf.append(w) + self.workflows = to_keep_wf + + def export_workflows_to_tsv(self, output_fp: str) -> None: + """ + Export workflows to a TSV file + """ + renaming = { + "name": "Name", + "source": "Source", + "id": "ID", + "link": "Link", + "creators": "Creators", + "tags": "Tags", + "create_time": "Creation time", + "update_time": "Update time", + "latest_version": "Latest version", + "versions": "Versions", + "number_of_steps": "Number of steps", + "tools": "Tools", + "edam_operation": "EDAM operations", + "edam_topic": "EDAM topics", + "license": "License", + "doi": "DOI", + } + + df = pd.DataFrame(self.export_workflows_to_dict()) + + for col in ["tools", "edam_operation", "edam_topic", "creators", "tags"]: + df[col] = shared.format_list_column(df[col]) + + df = df.rename(columns=renaming).fillna("").reindex(columns=list(renaming.values())) + df.to_csv(output_fp, sep="\t", index=False) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Extract Galaxy Workflows from WorkflowHub and public servers") + subparser = parser.add_subparsers(dest="command") + + # Extract Workflows + extract = subparser.add_parser("extract", help="Extract all workflows") + extract.add_argument("--all", "-o", required=True, help="Filepath to JSON with all extracted workflows") + extract.add_argument( + "--tools", + "-t", + required=True, + help="Filepath to JSON with all extracted tools, generated by extractools command", + ) + extract.add_argument( + "--test", + action="store_true", + default=False, + required=False, + help="Run a small test case only on one topic", + ) + + # Filter workflows + filterwf = subparser.add_parser("filter", help="Filter workflows based on their tags") + filterwf.add_argument( + "--all", + "-a", + required=True, + help="Filepath to JSON with all extracted workflows, generated by extract command", + ) + filterwf.add_argument( + "--filtered", + "-f", + required=True, + help="Filepath to TSV with filtered tutorials", + ) + filterwf.add_argument( + "--tags", + "-c", + help="Path to a file with tags to keep in the extraction (one per line)", + ) + + args = parser.parse_args() + + if args.command == "extract": + wfs = Workflows(test=args.test) + wfs.init_by_searching(args.tools) + shared.export_to_json(wfs.export_workflows_to_dict(), args.all) + + elif args.command == "filter": + wfs = Workflows() + wfs.init_by_importing(wfs=shared.load_json(args.all)) + tags = shared.read_file(args.tags) + wfs.filter_workflows_by_tags(tags) + wfs.export_workflows_to_tsv(args.filtered) diff --git a/sources/bin/extract_gtn_tutorials.py b/sources/bin/extract_gtn_tutorials.py index 2f43904f..0c66e486 100644 --- a/sources/bin/extract_gtn_tutorials.py +++ b/sources/bin/extract_gtn_tutorials.py @@ -34,10 +34,7 @@ def get_short_tool_ids(tuto: dict) -> None: tuto["short_tools"] = set() if "tools" in tuto: for tool in tuto["tools"]: - if "toolshed" in tool: - tuto["short_tools"].add(tool.split("/")[-2]) - else: - tuto["short_tools"].add(tool) + tuto["short_tools"].add(shared.shorten_tool_id(tool)) tuto["short_tools"] = list(tuto["short_tools"]) @@ -58,13 +55,7 @@ def get_edam_operations(tuto: dict, tools: dict) -> None: """ tuto["edam_operation"] = [] if "short_tools" in tuto: - edam_operation = set() - for t in tuto["short_tools"]: - if t in tools: - edam_operation.update(set(tools[t]["EDAM operation"])) - else: - print(f"{t} not found in all tools") - tuto["edam_operation"] = list(edam_operation) + tuto["edam_operation"] = shared.get_edam_operation_from_tools(tuto["short_tools"], tools) def get_feedback(tuto: dict, feedback: dict) -> None: diff --git a/sources/bin/get_community_workflows.sh b/sources/bin/get_community_workflows.sh new file mode 100644 index 00000000..6d00680d --- /dev/null +++ b/sources/bin/get_community_workflows.sh @@ -0,0 +1,39 @@ +#!/usr/bin/env bash + +if [ ! -z $1 ] +then + python sources/bin/extract_galaxy_workflows.py \ + filter \ + --all "communities/all/resources/test_workflows.json" \ + --filtered "communities/microgalaxy/resources/test_workflows.tsv" \ + --tags "communities/microgalaxy/metadata/workflow_tags" + + python sources/bin/create_interactive_table.py \ + --input "communities/microgalaxy/resources/test_workflows.tsv" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/microgalaxy/resources/workflows.html" + +else + for com_data_fp in data/communities/* ; do + if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then + community=`basename "$com_data_fp"` + + echo "$community"; + + if [[ -f "data/communities/$community/workflow_tags" ]]; then + mkdir -p "results/$community/" + + python sources/bin/extract_galaxy_workflows.py \ + filter \ + --all "communities/all/resources/workflows.json" \ + --filtered "communities/$community/resources/workflows.tsv" \ + --tags "communities/$community/metadata/workflow_tags" + + python sources/bin/create_interactive_table.py \ + --input "communities/$community/resources/workflows.tsv" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/$community/resources/workflows.html" + fi; + fi; + done +fi diff --git a/sources/bin/shared.py b/sources/bin/shared.py index f0aefc46..ee22c7f3 100644 --- a/sources/bin/shared.py +++ b/sources/bin/shared.py @@ -82,3 +82,29 @@ def get_request_json(url: str, headers: dict) -> dict: def format_date(date: str) -> str: return datetime.fromisoformat(date).strftime("%Y-%m-%d") + + +def shorten_tool_id(tool: str) -> str: + """ + Shorten tool id + """ + if "toolshed" in tool: + return tool.split("/")[-2] + else: + return tool + + +def get_edam_operation_from_tools(selected_tools: list, all_tools: dict) -> List: + """ + Get list of EDAM operations of the tools + + :param selected_tools: list of tool suite ids + :param all_tools: dictionary with information about all tools + """ + edam_operation = set() + for t in selected_tools: + if t in all_tools: + edam_operation.update(set(all_tools[t]["EDAM operation"])) + else: + print(f"{t} not found in all tools") + return list(edam_operation)