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Updating workflows/microbiome/allele-based-pathogen-identification from 0.1.2 to 0.1.3 #679

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Feb 27, 2025
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Updating workflows/microbiome/allele-based-pathogen-identification from 0.1.2 to 0.1.3 #679

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7ecd1e5
Updating workflows/microbiome/allele-based-pathogen-identification fr…
Feb 24, 2025
fd69b65
Fix name
mvdbeek Feb 27, 2025
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32 changes: 16 additions & 16 deletions ...s/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga
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Expand Up @@ -89,7 +89,7 @@
{
"class": "Person",
"identifier": "0000-0001-9852-1987",
"name": "Bérénice Batut",
"name": "B\u00e9r\u00e9nice Batut",
"url": "https://orcid.org/0000-0001-9852-1987"
},
{
Expand All @@ -100,7 +100,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.1.2",
"release": "0.1.3",
"name": "Allele-based Pathogen Identification",
"report": {
"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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"top": 35
},
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"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": true}",
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": true}",
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"type": "parameter_input",
"uuid": "d28b9bed-c674-406c-b58b-165bcc8eec17",
Expand Down Expand Up @@ -243,7 +243,7 @@
},
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Expand Down Expand Up @@ -295,15 +295,15 @@
"output_name": "alignment_output"
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"tool_version": "2.28+galaxy0",
"tool_version": "2.28+galaxy1",
"type": "tool",
"uuid": "6da37636-966d-4975-bce3-d650feaeb17c",
"when": null,
Expand All @@ -317,7 +317,7 @@
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"errors": null,
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"input_connections": {
Expand Down Expand Up @@ -379,15 +379,15 @@
"output_name": "pileup"
}
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"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+galaxy1",
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"tool_state": "{\"adv\": {\"qual\": \"0\", \"snp_min_af\": \"0.08\", \"indel_min_af\": \"0.15\", \"enable_phasing\": false, \"no_phasing_for_fa\": false, \"print_ref_calls\": false, \"ploidity_model\": \"--haploid_precise\", \"chunk_size\": \"5000000\"}, \"bam_input\": {\"__class__\": \"ConnectedValue\"}, \"bed_or_vcf\": {\"bed_or_vcf_selector\": \"unrestricted\", \"__current_case__\": 2, \"include_all_ctgs\": true}, \"gvcf\": false, \"model_source\": {\"source\": \"built-in\", \"__current_case__\": 0, \"select_built_in\": \"r941_prom_hac_g360+g422\"}, \"output_files\": [\"full_alignment\", \"pileup\"], \"ref_source\": {\"source\": \"history\", \"__current_case__\": 0, \"ref_fasta\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.8+galaxy1",
"tool_state": "{\"adv\": {\"qual\": \"0\", \"snp_min_af\": \"0.08\", \"indel_min_af\": \"0.15\", \"enable_phasing\": false, \"no_phasing_for_fa\": false, \"print_ref_calls\": false, \"ploidity_model\": \"--haploid_precise\", \"chunk_size\": \"5000000\"}, \"bam_input\": {\"__class__\": \"ConnectedValue\"}, \"bed_or_vcf\": {\"bed_or_vcf_selector\": \"unrestricted\", \"__current_case__\": 2, \"include_all_ctgs\": true}, \"gvcf\": false, \"model_source\": {\"source\": \"built-in\", \"__current_case__\": 0, \"select_built_in\": \"r941_prom_hac_g360+g422\"}, \"ont_license_agree\": false, \"output_files\": [\"full_alignment\", \"pileup\"], \"ref_source\": {\"source\": \"history\", \"__current_case__\": 0, \"ref_fasta\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.10+galaxy1",
"type": "tool",
"uuid": "ffbad354-41de-488d-bb37-929926bbfb31",
"when": null,
Expand Down Expand Up @@ -681,7 +681,7 @@
},
"12": {
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
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"errors": null,
"id": 12,
"input_connections": {
Expand Down Expand Up @@ -709,15 +709,15 @@
"top": 617.8951200002152
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1",
"tool_shed_repository": {
"changeset_revision": "3bf5661c0280",
"changeset_revision": "56a8da1f2243",
"name": "table_compute",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"out_opts\": [\"ignore_nas\"], \"precision\": \"2\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": null, \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": true}, \"user\": {\"mode\": \"matrixapply\", \"__current_case__\": 3, \"matrixapply_func\": {\"vector_op\": \"mean\", \"__current_case__\": 6}, \"dimension\": \"0\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.2.4+galaxy0",
"tool_version": "1.2.4+galaxy1",
"type": "tool",
"uuid": "b20b66f5-e975-4947-8935-8c628d016514",
"when": null,
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7 changes: 7 additions & 0 deletions workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md
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@@ -1,5 +1,12 @@
# Changelog

## [0.1.3] 2025-02-24

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1`

## [0.1.2] 2024-09-24

### Automatic update
Expand Down