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Merge pull request #496 from planemo-autoupdate/workflows/microbiome/…
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…allele-based-pathogen-identification

Updating workflows/microbiome/allele-based-pathogen-identification from 0.1.1 to 0.1.2
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@mvdbeek
mvdbeek authored Oct 29, 2024
2 parents 900635a + 7697559 commit ece941f
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48 changes: 24 additions & 24 deletions ...s/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga
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],
"format-version": "0.1",
"license": "MIT",
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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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8 changes: 8 additions & 0 deletions workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md
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# Changelog

## [0.1.2] 2024-09-24

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/0.1.12+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.8+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4`
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4`

## [0.1.1] 2024-06-28

### Automatic update
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