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Assembly-Hifi-Trio-phasing-VGP5.ga
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{
"a_galaxy_workflow": "true",
"annotation": "",
"comments": [],
"creator": [
{
"class": "Organization",
"name": "Galaxy"
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{
"class": "Organization",
"name": "VGP",
"url": "https://vertebrategenomeproject.org"
}
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"release": "0.9.0",
"name": "Genome Assembly with Pacbio Hifi reads and Trio data for phasing - VGP5",
"report": {
"markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\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_stats)\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\r\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\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```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
},
"steps": {
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"id": 0,
"input_connections": {},
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"name": "Pacbio Reads Collection : child"
}
],
"label": "Pacbio Reads Collection : child",
"name": "Input dataset collection",
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"position": {
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"input_connections": {},
"inputs": [
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"description": "",
"name": "Paternal Illumina reads (hap1)"
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],
"label": "Paternal Illumina reads (hap1)",
"name": "Input dataset collection",
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"input_connections": {},
"inputs": [
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"name": "Maternal Illumina reads (hap2)"
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],
"label": "Maternal Illumina reads (hap2)",
"name": "Input dataset collection",
"outputs": [],
"position": {
"left": 0,
"top": 428.5859375
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"input_connections": {},
"inputs": [
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"name": "Meryl Database : Child"
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"label": "Meryl Database : Child",
"name": "Input dataset",
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"inputs": [
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"name": "Hapmer Database : Paternal"
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],
"label": "Hapmer Database : Paternal",
"name": "Input dataset",
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"inputs": [
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"name": "Hapmer Database : Maternal"
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"label": "Hapmer Database : Maternal",
"name": "Input dataset",
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},
"6": {
"annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.",
"content_id": null,
"errors": null,
"id": 6,
"input_connections": {},
"inputs": [
{
"description": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.",
"name": "Bits for bloom filter"
}
],
"label": "Bits for bloom filter",
"name": "Input parameter",
"outputs": [],
"position": {
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"top": 890.2068997739406
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"tool_id": null,
"tool_state": "{\"default\": 37, \"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}",
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"id": 7,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "Database for Busco Lineage"
}
],
"label": "Database for Busco Lineage",
"name": "Input parameter",
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"top": 1078.9295496884674
},
"tool_id": null,
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
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"type": "parameter_input",
"uuid": "ca553be3-e5c9-4770-bd61-d50ed05c69ae",
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"8": {
"annotation": "Taxonomic lineage for the organism being assembled for Busco analysis",
"content_id": null,
"errors": null,
"id": 8,
"input_connections": {},
"inputs": [
{
"description": "Taxonomic lineage for the organism being assembled for Busco analysis",
"name": "Lineage"
}
],
"label": "Lineage",
"name": "Input parameter",
"outputs": [],
"position": {
"left": 61.152110333438976,
"top": 1189.4200518565176
},
"tool_id": null,
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
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"type": "parameter_input",
"uuid": "9762d451-eb6f-4f0c-8203-7094f46ea771",
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},
"9": {
"annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ",
"content_id": null,
"errors": null,
"id": 9,
"input_connections": {},
"inputs": [
{
"description": "If empty, read coverage will be estimated from the Genomescope parameters. ",
"name": "Homozygous Read Coverage"
}
],
"label": "Homozygous Read Coverage",
"name": "Input parameter",
"outputs": [],
"position": {
"left": 98.92882500063175,
"top": 1275.4014318043698
},
"tool_id": null,
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}",
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"uuid": "ffcf874f-594d-4d58-99dc-73ef566bcc88",
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},
"10": {
"annotation": "GenomeScope model parameters generated by K-mer profiling workflow",
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"id": 10,
"input_connections": {},
"inputs": [
{
"description": "GenomeScope model parameters generated by K-mer profiling workflow",
"name": "Genomescope Model Parameters"
}
],
"label": "Genomescope Model Parameters",
"name": "Input dataset",
"outputs": [],
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"inputs": [
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"name": "Genomescope Summary"
}
],
"label": "Genomescope Summary",
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"uuid": "81d79a21-1ba4-415c-a6ce-8a8e04ec6f59",
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},
"12": {
"annotation": "--trio-dual option",
"content_id": null,
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"id": 12,
"input_connections": {},
"inputs": [
{
"description": "--trio-dual option",
"name": "Utilize homology information to correct trio-phasing errors"
}
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"label": "Utilize homology information to correct trio-phasing errors",
"name": "Input parameter",
"outputs": [],
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"input_connections": {},
"inputs": [
{
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"name": "Name for Haplotype 1"
}
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"label": "Name for Haplotype 1",
"name": "Input parameter",
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"name": "Name for Haplotype 2"
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{
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{
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"post_job_actions": {
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"action_type": "HideDatasetAction",
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