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Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.13 to 0.3.14 #965

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Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.13 to 0.3.14 #965

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154 changes: 123 additions & 31 deletions workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga
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Original file line number Diff line number Diff line change
Expand Up @@ -516,7 +516,12 @@
"output_name": "output"
}
},
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"inputs": [
{
"description": "runtime parameter for tool Cutadapt",
"name": "library"
}
],
"label": null,
"name": "Cutadapt",
"outputs": [
Expand Down Expand Up @@ -598,7 +603,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Cutadapt",
"name": "library"
}
],
"label": null,
"name": "Cutadapt",
"outputs": [
Expand Down Expand Up @@ -784,7 +794,12 @@
"output_name": "report"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool MultiQC",
"name": "image_content_input"
}
],
"label": null,
"name": "MultiQC",
"outputs": [
Expand Down Expand Up @@ -1180,7 +1195,12 @@
"output_name": "text_param"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Map parameter value",
"name": "input_param_type"
}
],
"label": null,
"name": "Map parameter value",
"outputs": [
Expand Down Expand Up @@ -1231,7 +1251,12 @@
"output_name": "text_param"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Map parameter value",
"name": "input_param_type"
}
],
"label": null,
"name": "Map parameter value",
"outputs": [
Expand Down Expand Up @@ -1282,7 +1307,12 @@
"output_name": "text_param"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Map parameter value",
"name": "input_param_type"
}
],
"label": null,
"name": "Map parameter value",
"outputs": [
Expand Down Expand Up @@ -1324,7 +1354,7 @@
}
},
"tags": [],
"uuid": "5680eff4-e99b-4bea-b949-1de86b2d9dca"
"uuid": "eab73b5a-8954-48c4-a2f3-defeb11d1121"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -1962,7 +1992,24 @@
"output_name": "out1"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Hifiasm",
"name": "assembly_options"
},
{
"description": "runtime parameter for tool Hifiasm",
"name": "hic_partition"
},
{
"description": "runtime parameter for tool Hifiasm",
"name": "hic_partition"
},
{
"description": "runtime parameter for tool Hifiasm",
"name": "mode"
}
],
"label": "Hifiasm",
"name": "Hifiasm",
"outputs": [
Expand Down Expand Up @@ -2303,7 +2350,12 @@
"output_name": "hic_balanced_contig_hap2_graph"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": "gfastats gfa hap2 no sequences",
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -2417,7 +2469,12 @@
"output_name": "hic_balanced_contig_hap1_graph"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": "gfastats gfa hap1",
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -2477,7 +2534,12 @@
"output_name": "hic_balanced_contig_hap2_graph"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": "gfastats gfa hap2",
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -2537,7 +2599,12 @@
"output_name": "hic_balanced_contig_hap2_graph"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -2582,7 +2649,12 @@
"output_name": "hic_balanced_contig_hap1_graph"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": "gfastats gfa hap1 no sequences",
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -2642,7 +2714,12 @@
"output_name": "hic_balanced_contig_hap1_graph"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -3140,7 +3217,7 @@
}
},
"tags": [],
"uuid": "dd6c65bf-97d3-4548-b6e5-c97405e20729"
"uuid": "f0e935db-6930-483d-8ac3-b27b37de1e9d"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -3522,7 +3599,7 @@
}
},
"tags": [],
"uuid": "1cb14911-226b-4856-a624-a094f4c72db4"
"uuid": "50d3a5af-248b-4965-bc47-48fd64a193dc"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -4220,7 +4297,7 @@
}
},
"tags": [],
"uuid": "86022972-9e63-4a4f-b30c-db94426b6882"
"uuid": "34d4fbb2-0eb7-4178-ae51-637e6e2d7887"
},
"tool_id": null,
"type": "subworkflow",
Expand All @@ -4241,7 +4318,7 @@
},
"58": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2",
"errors": null,
"id": 58,
"input_connections": {
Expand All @@ -4258,7 +4335,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "lineage"
}
],
"label": "Busco Hap2",
"name": "Busco",
"outputs": [
Expand Down Expand Up @@ -4324,15 +4406,15 @@
"output_name": "summary_image"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2",
"tool_shed_repository": {
"changeset_revision": "4e70d88adf2f",
"changeset_revision": "c5a90fa4b8dd",
"name": "busco",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"cached_db\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"test\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.8.0+galaxy1",
"tool_version": "5.8.0+galaxy2",
"type": "tool",
"uuid": "08066bc3-0992-4606-844d-16be3c56691a",
"when": null,
Expand Down Expand Up @@ -4493,7 +4575,7 @@
},
"60": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2",
"errors": null,
"id": 60,
"input_connections": {
Expand All @@ -4510,7 +4592,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "lineage"
}
],
"label": "Busco Hap1",
"name": "Busco",
"outputs": [
Expand Down Expand Up @@ -4576,15 +4663,15 @@
"output_name": "summary_image"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2",
"tool_shed_repository": {
"changeset_revision": "4e70d88adf2f",
"changeset_revision": "c5a90fa4b8dd",
"name": "busco",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"cached_db\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"test\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.8.0+galaxy1",
"tool_version": "5.8.0+galaxy2",
"type": "tool",
"uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4",
"when": null,
Expand Down Expand Up @@ -4625,7 +4712,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Merqury",
"name": "mode"
}
],
"label": "Merqury",
"name": "Merqury",
"outputs": [
Expand Down Expand Up @@ -5313,7 +5405,7 @@
"VGP",
"Reviewed"
],
"uuid": "2eb08c5f-394b-4bd6-b7ad-35e26c66c6f6",
"uuid": "a27cd1d5-a95c-433e-a533-01b63d0d6c24",
"version": 1,
"release": "0.3.13"
}
"release": "0.3.14"
}
5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.3.14] - 2025-10-06

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2`

## [0.3.13] - 2025-09-29

### Automatic update
Expand Down