diff --git a/workflows/microbiome/nanopore-pre-processing/CHANGELOG.md b/workflows/microbiome/nanopore-pre-processing/CHANGELOG.md index 1e54ec9ff..e82e472ae 100644 --- a/workflows/microbiome/nanopore-pre-processing/CHANGELOG.md +++ b/workflows/microbiome/nanopore-pre-processing/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.1.1] 2024-08-26 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1` + ## [0.1] 2024-04-25 First release. diff --git a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga index 986f020ed..d9f20cd0e 100644 --- a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga +++ b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga @@ -192,7 +192,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.1.1", "name": "Nanopore Preprocessing", "report": { "markdown": "# Nanopore - Preprocessing Workflow Report\nBelow are the results of the Preprocessing 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\nA collection of all sample reads (all in the same sequence file format, e.g.: Fastq, Fastq.gz, Fastqsanger, etc.)\n\n## Workflow Outputs\n\n### Multi QC Report of all samples before reads quality retaining\n\n```galaxy\nhistory_dataset_as_image(output=\"multiQC_html_report_before_preprocessing\")\n```\n### Multi QC Report of all samples after reads quality retaining\n\n```galaxy\nhistory_dataset_as_image(output=\"multiQC_html_report_after_preprocessing\")\n```\n\n### Table of the total number of reads and the number of host reads\n\n```galaxy\nhistory_dataset_display(output=\"removed_hosts_percentage_tabular\")\n```\n\n" @@ -433,7 +433,7 @@ }, "5": { "annotation": "Quality Check Before Preprocessing", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -495,15 +495,15 @@ "output_name": "html_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "tool_shed_repository": { - "changeset_revision": "5ec9f6bceaee", + "changeset_revision": "2c64fded1286", "name": "fastqc", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.74+galaxy0", + "tool_version": "0.74+galaxy1", "type": "tool", "uuid": "b393d71b-0708-4825-97f2-d43a3f312f73", "when": null, @@ -852,7 +852,7 @@ }, "10": { "annotation": "Quality Check After Preprocessing", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "errors": null, "id": 10, "input_connections": { @@ -914,15 +914,15 @@ "output_name": "html_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "tool_shed_repository": { - "changeset_revision": "5ec9f6bceaee", + "changeset_revision": "2c64fded1286", "name": "fastqc", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.74+galaxy0", + "tool_version": "0.74+galaxy1", "type": "tool", "uuid": "2862f65a-7df0-4d6a-8aaf-caa677dd8bcf", "when": null, @@ -1249,7 +1249,7 @@ }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1", "errors": null, "id": 17, "input_connections": { @@ -1296,15 +1296,15 @@ "output_name": "report_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "20e2f64aa1fe", + "changeset_revision": "cdee7158adf3", "name": "kraken2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"kalamari\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": true, \"report_minimizer_data\": true}, \"single_paired\": {\"single_paired_selector\": \"no\", \"__current_case__\": 2, \"input_sequences\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.1.1+galaxy1", + "tool_version": "2.1.3+galaxy1", "type": "tool", "uuid": "2c6bbcf9-178e-4cc2-8340-385961c4bdb1", "when": null, @@ -1370,7 +1370,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "errors": null, "id": 19, "input_connections": { @@ -1425,15 +1425,15 @@ "output_name": "text_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "tool_shed_repository": { - "changeset_revision": "5ec9f6bceaee", + "changeset_revision": "2c64fded1286", "name": "fastqc", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.74+galaxy0", + "tool_version": "0.74+galaxy1", "type": "tool", "uuid": "7140e440-b547-4cae-baa0-89e29a3f2bda", "when": null,