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Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.3.4 to 0.3.5 #967

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Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.3.4 to 0.3.5 #967

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126 changes: 95 additions & 31 deletions workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga
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Original file line number Diff line number Diff line change
Expand Up @@ -457,7 +457,12 @@
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"name": "Cutadapt",
"outputs": [
Expand Down Expand Up @@ -688,7 +693,7 @@
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Expand All @@ -697,7 +702,12 @@
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{
"description": "runtime parameter for tool MultiQC",
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],
"label": null,
"name": "MultiQC",
"outputs": [
Expand All @@ -715,15 +725,15 @@
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Expand Down Expand Up @@ -1067,7 +1077,16 @@
"output_name": "out1"
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"description": "runtime parameter for tool Hifiasm",
"name": "assembly_options"
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{
"description": "runtime parameter for tool Hifiasm",
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"name": "Hifiasm",
"outputs": [
Expand Down Expand Up @@ -1226,7 +1245,12 @@
"output_name": "primary_contig_graph"
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"outputs": [
Expand Down Expand Up @@ -1286,7 +1310,12 @@
"output_name": "primary_contig_graph"
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"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -1346,7 +1375,12 @@
"output_name": "alternate_contig_graph"
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"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -1406,7 +1440,12 @@
"output_name": "alternate_contig_graph"
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"outputs": [
Expand Down Expand Up @@ -1466,7 +1505,12 @@
"output_name": "primary_contig_graph"
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Expand Down Expand Up @@ -1533,7 +1577,12 @@
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Expand Down Expand Up @@ -1809,7 +1858,7 @@
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"input_connections": {
Expand All @@ -1826,7 +1875,12 @@
"output_name": "output"
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"name": "lineage"
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"name": "Busco",
"outputs": [
Expand Down Expand Up @@ -1899,15 +1953,15 @@
"output_name": "summary_image"
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Expand Down Expand Up @@ -2080,7 +2134,12 @@
"output_name": "output"
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Expand Down Expand Up @@ -2197,7 +2256,7 @@
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"input_connections": {
Expand All @@ -2214,7 +2273,12 @@
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Expand Down Expand Up @@ -2287,15 +2351,15 @@
"output_name": "summary_image"
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},
"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}",
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Expand Down Expand Up @@ -2913,7 +2977,7 @@
}
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"type": "subworkflow",
Expand Down Expand Up @@ -3295,7 +3359,7 @@
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Expand Down Expand Up @@ -4092,7 +4156,7 @@
}
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Expand Down Expand Up @@ -4227,7 +4291,7 @@
"VGP",
"Reviewed"
],
"uuid": "40ef3ef9-6781-42d6-baf0-70fe10cc9622",
"uuid": "5be7e9a2-d9b9-479c-907c-0e5249bf15da",
"version": 1,
"release": "0.3.4"
}
"release": "0.3.5"
}
6 changes: 6 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md
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@@ -1,5 +1,11 @@
# Changelog

## [0.3.5] - 2025-10-13

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4`
- `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`

## [0.3.4] - 2025-09-29

### Automatic update
Expand Down