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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 Sep 23, 2024
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# Changelog

## [0.4.3] 2024-09-23

### 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`
- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1`
- `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`

## [0.4.2] 2024-03-06

### Automatic update
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"format-version": "0.1",
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"name": "COVID-19: consensus construction",
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"release": "0.4.3",
"steps": {
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"annotation": "Collection of VCFs produced by upstream workflows for variation analysis",
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},
"8": {
"annotation": "",
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"id": 8,
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"output_name": "output"
}
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{
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"name": "filter_expression"
},
{
"description": "runtime parameter for tool SnpSift Filter",
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}
],
"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"
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{
"description": "runtime parameter for tool Filter",
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"name": "Filter",
"outputs": [
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"output_name": "output"
}
},
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{
"description": "runtime parameter for tool SnpSift Extract Fields",
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"outputs": [
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"output_name": "output"
}
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"description": "runtime parameter for tool SnpSift Extract Fields",
"name": "input"
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"outputs": [
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},
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Expand All @@ -709,12 +682,7 @@
"output_name": "output"
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}
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"name": "Compute",
"outputs": [
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"output_name": "out_file1"
}
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"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "fd260e32-723d-4a22-8d64-4795557f8159",
"when": null,
Expand All @@ -765,7 +733,7 @@
},
"16": {
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"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"errors": null,
"id": 16,
"input_connections": {
Expand All @@ -774,12 +742,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Compute",
"outputs": [
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"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"tool_shed_repository": {
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"changeset_revision": "aff5135563c6",
"name": "column_maker",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "116e8e99-53ca-4366-a7e1-e3a9fb0bcfc3",
"when": null,
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"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Concatenate",
"name": "input1"
},
{
"description": "runtime parameter for tool Concatenate",
"name": "input2"
}
],
"inputs": [],
"label": null,
"name": "Concatenate",
"outputs": [
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Merge",
"name": "input1"
}
],
"inputs": [],
"label": null,
"name": "Merge",
"outputs": [
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"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Subtract",
"name": "input1"
},
{
"description": "runtime parameter for tool Subtract",
"name": "input2"
}
],
"inputs": [],
"label": null,
"name": "Subtract",
"outputs": [
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},
"20": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
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"errors": null,
"id": 20,
"input_connections": {
Expand All @@ -1036,12 +976,7 @@
"output_name": "output"
}
},
"inputs": [
{
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"name": "input"
}
],
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"label": null,
"name": "Compute",
"outputs": [
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"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
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},
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"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "e06fe045-f0f0-4c32-80ad-a8e070946a2f",
"when": null,
Expand All @@ -1092,7 +1027,7 @@
},
"21": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
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"errors": null,
"id": 21,
"input_connections": {
Expand All @@ -1110,10 +1045,6 @@
}
},
"inputs": [
{
"description": "runtime parameter for tool bcftools consensus",
"name": "input_file"
},
{
"description": "runtime parameter for tool bcftools consensus",
"name": "reference_source"
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"output_name": "output_file"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
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"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\": true, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"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\": \"\", \"exclude\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.15.1+galaxy3",
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"uuid": "698a9a8c-f6fe-430b-a7e0-cf9e1d058d02",
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Expand All @@ -1175,12 +1106,7 @@
"output_name": "output_file"
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{
"description": "runtime parameter for tool Collapse Collection",
"name": "input_list"
}
],
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"label": null,
"name": "Collapse Collection",
"outputs": [
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