Updating workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation from 0.1 to 0.2

workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.2] 2024-06-28
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0`
+
 ## [0.1] 2024-04-24
 
 First release.

workflows/microbiome/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": "0.2",
     "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"
@@ -1474,7 +1474,7 @@
         },
         "36": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0",
             "errors": null,
             "id": 36,
             "input_connections": {
@@ -1506,15 +1506,15 @@
                 "top": 1132.9745890557185
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "a1a923cd89e8",
+                "changeset_revision": "64e2edfe7a2c",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": false, \"nameOnly\": false, \"split\": false, \"strand\": false, \"tab\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.30.0+galaxy1",
+            "tool_version": "2.31.1+galaxy0",
             "type": "tool",
             "uuid": "8018f07e-551c-4fef-b7ef-42589ff5b59e",
             "when": null,
@@ -1576,7 +1576,7 @@
         },
         "38": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0",
             "errors": null,
             "id": 38,
             "input_connections": {
@@ -1608,15 +1608,15 @@
                 "top": 1800.0079752861873
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "a1a923cd89e8",
+                "changeset_revision": "64e2edfe7a2c",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": false, \"nameOnly\": false, \"split\": false, \"strand\": false, \"tab\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.30.0+galaxy1",
+            "tool_version": "2.31.1+galaxy0",
             "type": "tool",
             "uuid": "d9d6c096-58e0-4a33-af38-e94709c9af3b",
             "when": null,
@@ -1822,7 +1822,7 @@
         },
         "43": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0",
             "errors": null,
             "id": 43,
             "input_connections": {
@@ -1862,15 +1862,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "a1a923cd89e8",
+                "changeset_revision": "64e2edfe7a2c",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": false, \"nameOnly\": false, \"split\": false, \"strand\": false, \"tab\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.30.0+galaxy1",
+            "tool_version": "2.31.1+galaxy0",
             "type": "tool",
             "uuid": "7283594d-0455-4f60-98f5-d9c315e28ee4",
             "when": null,