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Updating workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-fr…
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…om-variation from 0.4.2 to 0.4.3
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planemo-autoupdate committed May 27, 2024
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5 changes: 5 additions & 0 deletions ...ows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md
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# Changelog

## [0.4.3] 2024-05-27

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`

## [0.4.2] 2024-03-06

### Automatic update
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104 changes: 15 additions & 89 deletions ...ars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
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"format-version": "0.1",
"license": "MIT",
"name": "COVID-19: consensus construction",
"release": "0.4.2",
"release": "0.4.3",
"steps": {
"0": {
"annotation": "Collection of VCFs produced by upstream workflows for variation analysis",
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},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1",
"errors": null,
"id": 8,
"input_connections": {
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"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1",
"tool_shed_repository": {
"changeset_revision": "a1a923cd89e8",
"changeset_revision": "64e2edfe7a2c",
"name": "bedtools",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"d\": false, \"dz\": false, \"five\": false, \"input_type\": {\"input_type_select\": \"bam\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"report\": {\"report_select\": \"bg\", \"__current_case__\": 0, \"zero_regions\": true, \"scale\": \"1.0\"}, \"split\": true, \"strand\": \"\", \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.30.0",
"tool_version": "2.31.1",
"type": "tool",
"uuid": "d89684f5-5a49-4b4c-821b-6c8a87f3a46e",
"when": null,
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{
"description": "runtime parameter for tool SnpSift Filter",
"name": "filter_expression"
},
{
"description": "runtime parameter for tool SnpSift Filter",
"name": "input"
}
],
"label": null,
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{
"description": "runtime parameter for tool SnpSift Filter",
"name": "filter_expression"
},
{
"description": "runtime parameter for tool SnpSift Filter",
"name": "input"
}
],
"label": null,
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Filter",
"name": "cond"
},
{
"description": "runtime parameter for tool Filter",
"name": "input"
}
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"inputs": [],
"label": null,
"name": "Filter",
"outputs": [
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool SnpSift Extract Fields",
"name": "input"
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"name": "SnpSift Extract Fields",
"outputs": [
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"output_name": "output"
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},
"inputs": [
{
"description": "runtime parameter for tool SnpSift Extract Fields",
"name": "input"
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"name": "SnpSift Extract Fields",
"outputs": [
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
}
],
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"label": null,
"name": "Compute",
"outputs": [
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"output_name": "output"
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},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
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"label": null,
"name": "Compute",
"outputs": [
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"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Concatenate",
"name": "input1"
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{
"description": "runtime parameter for tool Concatenate",
"name": "input2"
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"name": "Concatenate",
"outputs": [
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"output_name": "output"
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"description": "runtime parameter for tool Merge",
"name": "input1"
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"output_name": "out_file1"
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"inputs": [
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"description": "runtime parameter for tool Subtract",
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{
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"name": "Subtract",
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"output_name": "output"
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"inputs": [
{
"description": "runtime parameter for tool Compute",
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"name": "Compute",
"outputs": [
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}
},
"inputs": [
{
"description": "runtime parameter for tool bcftools consensus",
"name": "input_file"
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{
"description": "runtime parameter for tool bcftools consensus",
"name": "reference_source"
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"output_name": "output_file"
}
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"inputs": [
{
"description": "runtime parameter for tool Collapse Collection",
"name": "input_list"
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],
"inputs": [],
"label": null,
"name": "Collapse Collection",
"outputs": [
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