diff --git a/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md b/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md index f17daf4ca3..4b99b15cb0 100644 --- a/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md +++ b/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md @@ -1,5 +1,10 @@ # 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. diff --git a/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga b/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga index 02fa90d5ac..8410271bf6 100644 --- a/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga +++ b/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga @@ -202,7 +202,7 @@ ], "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" @@ -2402,7 +2402,7 @@ }, "55": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3", "errors": null, "id": 55, "input_connections": { @@ -2438,9 +2438,9 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3", "tool_shed_repository": { - "changeset_revision": "e005e659ae21", + "changeset_revision": "bc939965ce41", "name": "fasttree", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2871,7 +2871,7 @@ }, "66": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3", "errors": null, "id": 66, "input_connections": { @@ -2899,9 +2899,9 @@ "top": 1184.9745890557185 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3", "tool_shed_repository": { - "changeset_revision": "e005e659ae21", + "changeset_revision": "bc939965ce41", "name": "fasttree", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2915,7 +2915,7 @@ }, "67": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3", "errors": null, "id": 67, "input_connections": { @@ -2943,9 +2943,9 @@ "top": 1852.0079752861873 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3", "tool_shed_repository": { - "changeset_revision": "e005e659ae21", + "changeset_revision": "bc939965ce41", "name": "fasttree", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"