Updating workflows/microbiome/pathogen-identification/gene-based-pathogen-identification from 0.1 to 0.2

Author: planemo-autoupdate

workflows/microbiome/pathogen-identification/gene-based-pathogen-identification/CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.2] - 2026-01-19
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.6+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/2.1.1+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3`
+
 ## [0.1] - 2024-04-18
 
 First release.

workflows/microbiome/pathogen-identification/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga

@@ -111,7 +111,6 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
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     "name": "Gene-based Pathogen Identification",
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         "markdown": "# Gene-based Pathogen Identification Workflow Report\n\nBelow are the results for the Gene based Pathogen Identification 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\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Output\n\n### Identified contigs per sample\n\n```galaxy\nhistory_dataset_display(output=\"contigs\")\n```\n\n### Identified pathogenic genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"vfs\")\n```\n\n### Identified Antimicrobial Resistance genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"amrs\")\n```\n"
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