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Updating workflows/microbiome/pathogen-identification/allele-based-pathogen-identification from 0.1.4 to 0.1.5 #862

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Updating workflows/microbiome/pathogen-identification/allele-based-pathogen-identification from 0.1.4 to 0.1.5 #862

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72 changes: 36 additions & 36 deletions ...entification/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga
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],
"format-version": "0.1",
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"name": "Allele-based Pathogen Identification",
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"markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic 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), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage percentage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n"
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10 changes: 10 additions & 0 deletions ...biome/pathogen-identification/allele-based-pathogen-identification/CHANGELOG.md
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# Changelog

## [0.1.5] - 2025-10-08

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.21+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.21+galaxy3`
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2`
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- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy2`

## [0.1.4] - 2025-03-10

### Automatic update
Expand Down