diff --git a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga index a41070e3f..2ef573362 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga +++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga @@ -100,7 +100,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1.1", + "release": "0.1.2", "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" @@ -317,7 +317,7 @@ }, "5": { "annotation": "", - 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"tool_version": "0.1.12+galaxy0", + "tool_version": "1.0.8+galaxy1", "type": "tool", "uuid": "ffbad354-41de-488d-bb37-929926bbfb31", "when": null, @@ -494,7 +494,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "errors": null, "id": 8, "input_connections": { @@ -534,15 +534,15 @@ "output_name": "output_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "tool_shed_repository": { - "changeset_revision": "ebb2e12a6de1", + "changeset_revision": "271965b55437", "name": "bcftools_norm", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"atomize\": false, \"check_ref\": \"w\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"multiallelics\": {\"mode\": \"\", \"__current_case__\": 0}, \"normalize_indels\": false, \"old_rec_tag\": \"\", \"output_type\": \"v\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rm_dup\": \"\", \"sec_default\": {\"site_win\": \"1000\"}, \"sec_restrict\": {\"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"regions_overlap\": null, \"targets\": {\"targets_src\": \"__none__\", \"__current_case__\": 0}, \"targets_overlap\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy3", + "tool_version": "1.15.1+galaxy4", "type": "tool", "uuid": "9a34ec91-725e-49b2-973b-1c508e4bdc5d", "when": null, @@ -556,7 +556,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "errors": null, "id": 9, "input_connections": { @@ -579,15 +579,15 @@ "top": 623.8951200002152 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": \"1,2\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", + "tool_version": "9.3+galaxy2", "type": "tool", "uuid": "f6f94754-2660-4fe4-b1dc-937728fc898f", "when": null, @@ -818,7 +818,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "errors": null, "id": 15, "input_connections": { @@ -862,15 +862,15 @@ "output_name": "output_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "tool_shed_repository": { - "changeset_revision": "147de996e34f", + "changeset_revision": "8aa352093d73", "name": "bcftools_consensus", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": false, \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": false, \"sample\": \"\", \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": null, \"exclude\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy3", + "tool_version": "1.15.1+galaxy4", "type": "tool", "uuid": "872ba641-1909-43ea-b3c2-62e6773583a6", "when": null, @@ -909,7 +909,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1049,7 +1049,7 @@ }, "20": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "errors": null, "id": 20, "input_connections": { @@ -1072,15 +1072,15 @@ "top": 949.9024800002072 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": \"1\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", + "tool_version": "9.3+galaxy2", "type": "tool", "uuid": "74036007-7df4-4e3f-86c3-e73f511bdbbe", "when": null, @@ -1204,7 +1204,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1324,4 +1324,4 @@ ], "uuid": "435875a1-72c4-4fda-8943-3a78f25c6574", "version": 72 -} +} \ No newline at end of file diff --git a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md index e13bf3593..d75f39c85 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md @@ -1,5 +1,13 @@ # 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