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Updating workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-…
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…wgs-variant-calling from 0.1.5 to 0.1.6
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planemo-autoupdate committed Jan 27, 2025
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# Changelog

## [0.1.6] 2025-01-27

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3`
- `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3`

## [0.1.5] 2024-03-05

### Automatic update
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"format-version": "0.1",
"license": "MIT",
"name": "COVID-19: variation analysis on WGS SE data",
"release": "0.1.5",
"release": "0.1.6",
"steps": {
"0": {
"annotation": "Illumina reads with fastqsanger encoding",
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},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3",
"errors": null,
"id": 2,
"input_connections": {
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"output_name": "out1"
}
},
"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/0.24.0+galaxy3",
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"changeset_revision": "c59d48774d03",
"changeset_revision": "a626e8c0e1ba",
"name": "fastp",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"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\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.23.4+galaxy0",
"tool_version": "0.24.0+galaxy3",
"type": "tool",
"uuid": "226bdff2-28d7-46ec-9a17-887d577056f6",
"when": null,
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},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1",
"errors": null,
"id": 3,
"input_connections": {
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"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "0d4acadabb04",
"changeset_revision": "d5ceb9f3c25b",
"name": "bowtie2",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"set_id_auto\", \"__current_case__\": 2}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.5.3+galaxy0",
"tool_version": "2.5.3+galaxy1",
"type": "tool",
"uuid": "befd5b2a-7f19-48bf-9133-55dddc3791f2",
"when": null,
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool MarkDuplicates",
"name": "inputFile"
}
],
"inputs": [],
"label": null,
"name": "MarkDuplicates",
"outputs": [
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},
"5": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
"errors": null,
"id": 5,
"input_connections": {
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"label": null,
"name": "MultiQC",
"outputs": [
{
"name": "stats",
"type": "input"
},
{
"name": "html_report",
"type": "html"
},
{
"name": "stats",
"type": "tabular"
}
],
"position": {
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"output_name": "html_report"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
"tool_shed_repository": {
"changeset_revision": "abfd8a6544d7",
"changeset_revision": "a7e081ceb76a",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.11+galaxy1",
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.27+galaxy0",
"type": "tool",
"uuid": "cba65a56-8563-4777-8a87-b4c0158d8015",
"when": null,
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}
},
"inputs": [
{
"description": "runtime parameter for tool Realign reads",
"name": "reads"
},
{
"description": "runtime parameter for tool Realign reads",
"name": "reference_source"
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Insert indel qualities",
"name": "reads"
}
],
"inputs": [],
"label": null,
"name": "Insert indel qualities",
"outputs": [
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},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3",
"errors": null,
"id": 8,
"input_connections": {
Expand All @@ -488,10 +474,6 @@
}
},
"inputs": [
{
"description": "runtime parameter for tool Call variants",
"name": "reads"
},
{
"description": "runtime parameter for tool Call variants",
"name": "reference_source"
Expand All @@ -510,15 +492,15 @@
"top": 733.734375
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3",
"tool_shed_repository": {
"changeset_revision": "4805fe3d8fda",
"changeset_revision": "b11e8e9c23bf",
"name": "lofreq_call",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"call_control\": {\"set_call_options\": \"yes\", \"__current_case__\": 1, \"coverage\": {\"min_cov\": \"5\", \"max_depth\": \"1000000\"}, \"pe\": {\"use_orphan\": false}, \"bc_quals\": {\"min_bq\": \"30\", \"min_alt_bq\": \"30\", \"alt_bq\": {\"modify\": \"\", \"__current_case__\": 0}}, \"align_quals\": {\"alnqual\": {\"use_alnqual\": \"\", \"__current_case__\": 0, \"alnqual_choice\": {\"alnquals_to_use\": \"\", \"__current_case__\": 1, \"extended_baq\": true}}}, \"map_quals\": {\"min_mq\": \"20\", \"use_mq\": {\"no_mq\": \"\", \"__current_case__\": 0, \"max_mq\": \"255\"}}, \"source_qual\": {\"use_src_qual\": {\"src_qual\": \"\", \"__current_case__\": 0}}, \"joint_qual\": {\"min_jq\": \"0\", \"min_alt_jq\": \"0\", \"def_alt_jq\": \"0\"}}, \"filter_control\": {\"filter_type\": \"set_custom\", \"__current_case__\": 3, \"sig\": \"0.0005\", \"bonf\": \"0\", \"others\": false}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"regions\": {\"restrict_to_region\": \"genome\", \"__current_case__\": 0}, \"variant_types\": \"--call-indels\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.1.5+galaxy2",
"tool_version": "2.1.5+galaxy3",
"type": "tool",
"uuid": "c1515432-2f61-498d-9dcd-b44da6f923c7",
"when": null,
Expand All @@ -541,12 +523,7 @@
"output_name": "variants"
}
},
"inputs": [
{
"description": "runtime parameter for tool Lofreq filter",
"name": "invcf"
}
],
"inputs": [],
"label": null,
"name": "Lofreq filter",
"outputs": [
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}
},
"inputs": [
{
"description": "runtime parameter for tool SnpEff eff:",
"name": "input"
},
{
"description": "runtime parameter for tool SnpEff eff:",
"name": "intervals"
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