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Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.3.5 to 0.3.6
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‎workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga‎

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"format-version": "0.1",
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"license": "CC-BY-4.0",
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"name": "Genome Assembly from Hifi reads - VGP3",
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"readme": "## Contiging Solo:\n\nGenerate assembly based on PacBio Hifi Reads.\n\n\n### Inputs\n\n1. Species Name [text]\n2. Assembly Name [text]\n3. Hifi long reads [fastq collection]\n4. K-mer database [meryldb]\n5. Genome profile summary generated by Genomescope [txt]\n6. Bits for Hifiasm bloom filter [integer]\n7. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inaccurate [integer]\n8. Genomescope Model Parameters generated by Genomescope [tabular]\n9. Database for Compleasm lineage (recommended: latest)\n10. Compleasm lineage (recommended: vertebrata)\n11. Name of primary assembly\n12. Name of alternate assembly\n\n\n### Outputs\n\n1. Primary assembly\n2. Alternate assembly\n3. QC: Bandage image for the raw unitigs\n4. QC: Compleasm report for both assemblies\n5. QC: Merqury report for both assemblies\n6. QC: Assembly statistics for both assemblies\n7. QC: Nx and Size plots for both assemblies\n",
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"report": {
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"markdown": "Species:\n\n```galaxy\nhistory_dataset_embedded(output=\"Species Name for report\")\n```\n\n\nAssembly:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Name for report\")\n```\n\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\n\n```galaxy\nhistory_dataset_as_image(output=N)\n```\n\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\n## Compleasm results \n\nDatabase:\n\n```galaxy\nhistory_dataset_embedded(output=\"Lineage for report\")\n```\n\nPrimary Assembly\n\n\n```galaxy\nhistory_dataset_embedded(output=\"Compleasm on Primary Assembly contigs: Summary\")\n```\n\n\nAlternate Assembly\n\n\n```galaxy\nhistory_dataset_embedded(output=\"Compleasm on Alternate Assembly contigs: Summary\")\n```\n\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Nx and Size plots\")\n```\r\n\n\n\n\n"
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"readme": "## Contiging Solo:\n\nGenerate assembly based on PacBio Hifi Reads.\n\n\n### Inputs\n\n1. Species Name [text]\n2. Assembly Name [text]\n3. Hifi long reads [fastq collection]\n4. K-mer database [meryldb]\n5. Genome profile summary generated by Genomescope [txt]\n6. Bits for Hifiasm bloom filter [integer]\n7. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inaccurate [integer]\n8. Genomescope Model Parameters generated by Genomescope [tabular]\n9. Database for Compleasm lineage (recommended: latest)\n10. Compleasm lineage (recommended: vertebrata)\n11. Name of primary assembly\n12. Name of alternate assembly\n\n\n### Outputs\n\n1. Primary assembly\n2. Alternate assembly\n3. QC: Bandage image for the raw unitigs\n4. QC: Compleasm report for both assemblies\n5. QC: Merqury report for both assemblies\n6. QC: Assembly statistics for both assemblies\n7. QC: Nx and Size plots for both assemblies\n"
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‎workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md‎

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# Changelog
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## [0.3.6] - 2026-03-16
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### Automatic update
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- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3`
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## [0.3.5] - 2026-03-12
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### Changed

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