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Updating workflows/microbiome/gene-based-pathogen-identification from 0.1 to 0.2 #457

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Updating workflows/microbiome/gene-based-pathogen-identification from 0.1 to 0.2 #457

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589bd96
Updating workflows/microbiome/gene-based-pathogen-identification from…
Jun 28, 2024
cdd8660
Update Gene-based-Pathogen-Identification.ga
bebatut Jul 3, 2024
66f0c31
Apply suggestions from code review
bebatut Jul 10, 2024
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8 changes: 8 additions & 0 deletions workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md
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# Changelog

## [0.2] 2024-06-28
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### 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/2.9.3+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/1.7.2+galaxy1`
- `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/9.3+galaxy1`

## [0.1] 2024-04-18

First release.
54 changes: 27 additions & 27 deletions ...flows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga
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],
"format-version": "0.1",
"license": "MIT",
"release": "0.1",
"release": "0.2",
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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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Expand All @@ -304,7 +304,7 @@
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Expand All @@ -845,7 +845,7 @@
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Expand All @@ -902,7 +902,7 @@
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Expand All @@ -966,7 +966,7 @@
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