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Update workflow tests
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@bebatut
bebatut committed Dec 22, 2024
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12 changes: 12 additions & 0 deletions communities/microgalaxy/metadata/test_workflow_status.tsv
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Link Name Source Projects Creators Creation time Update time To keep Deprecated
https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Halophiles workup of Comparative gene analysis https://usegalaxy.eu Anton Nekrutenko 2024-12-03 2024-12-05 True False
https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 pAllori Blood RNA https://usegalaxy.eu Engy Nasr, Paul Zierep 2023-07-02 2024-11-24 True False
https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Metaproteomics workflow https://usegalaxy.eu Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Feature-Count Table Normalization https://usegalaxy.eu Johannes Effenberger 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 metaQuantome_datacreation_workflow https://usegalaxy.eu Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 metaquantome-function-worklow https://usegalaxy.eu Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu Engy Nasr, Paul Zierep 2023-06-30 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Metatranscriptomics data analysis https://usegalaxy.eu Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False
https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False
12 changes: 12 additions & 0 deletions communities/microgalaxy/resources/test_curated_workflows.tsv
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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
Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column True False
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 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT True False
Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT True False
Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT True False
metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT True False
metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT True False
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 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT True False
Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT True False
Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT True False
Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT True False
Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT True False
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