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Tool updates (no expected functional changes) to PE ARTIC WF
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wm75 committed Oct 1, 2024
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# Changelog

## [0.5.3] 2024-10-01

### Tool updates

- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0` updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0` updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1`

## [0.5.2] 2024-03-05

### Automatic update
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"format-version": "0.1",
"license": "MIT",
"name": "COVID-19: variation analysis on ARTIC PE data",
"release": "0.5.2",
"release": "0.5.3",
"steps": {
"0": {
"annotation": "Illumina reads from ARTIC assay with fastqsanger encoding",
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},
"8": {
"annotation": "",
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"errors": null,
"id": 8,
"input_connections": {
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"output_name": "report_json"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1",
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"changeset_revision": "d60c3f704da0",
"name": "fastp",
"owner": "iuc",
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},
"tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.23.4+galaxy0",
"tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.23.4+galaxy1",
"type": "tool",
"uuid": "849d9cac-14b8-4e45-823d-5747709e8b60",
"when": null,
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},
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"errors": null,
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"input_connections": {
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"top": 745.546875
},
"post_job_actions": {},
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"tool_shed_repository": {
"changeset_revision": "12615d397df7",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^##INFO=<ID=AmpliconBias,.+$\", \"replace_pattern\": \"##INFO=<ID=AmpliconBias,Number=0,Type=Flag,Description=\\\"Indicates that the AF value of the variant could not be corrected for potential amplicon bias.\\\">\"}, {\"__index__\": 1, \"find_pattern\": \"^##INFO=<ID=AF,.+$\", \"replace_pattern\": \"##INFO=<ID=AF,Number=1,Type=Float,Description=\\\"Lofreq Allele Frequency; Fraction of variant-supporting bases with q > --min-bq among all bases at the site\\\">\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy0",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "490dbabb-04ee-426d-a8e5-e2ec9e59de3a",
"when": null,
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"covid19.galaxyproject.org"
],
"uuid": "864427b0-d25a-499c-b437-f83f2d6b83f2"
}
}

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