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Update fasttree 2.1.10+galaxy1 to 2.1.10+galaxy3 in PathoGFAIR workflow. #1162

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Update fasttree 2.1.10+galaxy1 to 2.1.10+galaxy3 in PathoGFAIR workflow. #1162

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5 changes: 5 additions & 0 deletions ...athogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md
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# Changelog

## [0.1.1] - 2026-03-19

### Changed
- Update fasttree from 2.1.10+galaxy1 to 2.1.10+galaxy3

## [0.1] - 2024-04-24

First release.
20 changes: 10 additions & 10 deletions ...-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga
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],
"format-version": "0.1",
"license": "MIT",
"release": "0.1",
"release": "0.1.1",
"name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
"report": {
"markdown": "# Pathogen Detection - PathoGFAIR Samples Aggregation and Visualisation Workflow Report\nBelow are the results for the PathoGFAIR Samples Aggregation and Visualisation Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nTabular files and a FASTA file from the Gene-based Pathogen Identification workflow, four other tabular files from Nanopore Preprocessing and Nanopore - Allele-based Pathogen Identification workflow, and an optional Metadata tabular file with more sample information:\n\nFrom Gene-based Pathogenic Identification workflow: \n- contigs, FASTA file\n- VFs, Tabular file\n- vfs_of_genes_identified_by_vfdb, Tabular file\n- AMRs, Tabular file\n- amr_identified_by_ncbi, Tabular file\n\nFrom Nanopore - Allele bases Pathogen Identification workflow: \n- number_of_variants_per_sample, Tabular file\n- mapping_mean_depth_per_sample, Tabular file\n- mapping_coverage_percentage_per_sample, Tabular file\n\nFrom Nanopore Preprocessing: \n- removed_hosts_percentage_tabular, Tabular file\n\n## Some of the Workflow Outputs\n\n1- All Samples VFs Heatmap\n\n```galaxy\nhistory_dataset_as_image(output=\"heatmap_png\")\n```\n\n2- All samples phylogenetic tree VFs based\n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_vfs\")\n```\n\n3- All samples Phylogenetic tree AMR based \n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_amrs\")\n```\n\n4- Bar-plot for the Number of reads before host sequences removal and Number of found host reads per sample, performed in the Nanopore - Preprocessing workflow\n\n\n5- Barplot for the total number of removed host sequences per sample\n\n \n6- Barplot for the Mapping mean depth of coverage per sample\n\n\n6- Barplot for the Mapping breadth of coverage percentage per sample\n\n\n7- Barplot for the total number of complex variants and SNPs identified per sample\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"
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