Skip to content

Commit

Permalink
Updating workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5 fr…
Browse files Browse the repository at this point in the history 
…om 0.2 to 0.3
  • Loading branch information
planemo-autoupdate committed Aug 19, 2024
1 parent 425856c commit ae2cebc
Show file tree
Hide file tree
Showing 2 changed files with 99 additions and 25 deletions.
119 changes: 94 additions & 25 deletions workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"release": "0.2",
"release": "0.3",
"name": "Assembly-Hifi-Trio-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"
Expand Down Expand Up @@ -512,7 +512,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Cutadapt",
"name": "library"
}
],
"label": null,
"name": "Cutadapt",
"outputs": [
Expand Down Expand Up @@ -652,7 +657,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -790,7 +795,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1001,7 +1006,20 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Hifiasm",
"name": "assembly_options"
},
{
"description": "runtime parameter for tool Hifiasm",
"name": "mode"
},
{
"description": "runtime parameter for tool Hifiasm",
"name": "mode"
}
],
"label": null,
"name": "Hifiasm",
"outputs": [
Expand Down Expand Up @@ -1161,7 +1179,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -1225,7 +1248,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -1342,7 +1370,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -1420,7 +1453,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -1698,7 +1736,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "lineage"
},
{
"description": "runtime parameter for tool Busco",
"name": "lineage_conditional"
}
],
"label": null,
"name": "Busco",
"outputs": [
Expand Down Expand Up @@ -1813,7 +1860,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "lineage"
},
{
"description": "runtime parameter for tool Busco",
"name": "lineage_conditional"
}
],
"label": null,
"name": "Busco",
"outputs": [
Expand Down Expand Up @@ -1936,7 +1992,20 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Merqury",
"name": "mode"
},
{
"description": "runtime parameter for tool Merqury",
"name": "mode"
},
{
"description": "runtime parameter for tool Merqury",
"name": "mode"
}
],
"label": null,
"name": "Merqury",
"outputs": [
Expand Down Expand Up @@ -2192,7 +2261,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -2437,7 +2506,7 @@
}
},
"tags": [],
"uuid": "3eb2dea6-2727-4314-b65d-ee31a27df34d"
"uuid": "d4c0bf6f-e949-4c9f-b943-d6d509cc1591"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -2574,7 +2643,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -2819,7 +2888,7 @@
}
},
"tags": [],
"uuid": "8be9135a-1c67-4318-8bb0-a1db59e47933"
"uuid": "8a87a955-46c7-4508-bbb1-0d4908c9bec9"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -2860,7 +2929,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -2905,7 +2974,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -3499,7 +3568,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -3711,7 +3780,7 @@
}
},
"tags": [],
"uuid": "c0b11d93-b596-47ae-b5e1-7b67b4117a99"
"uuid": "8f0d2943-ca44-4f82-b11d-7ed59fcc0161"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -3785,7 +3854,7 @@
},
"52": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2",
"errors": null,
"id": 52,
"input_connections": {
Expand Down Expand Up @@ -3823,15 +3892,15 @@
"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": [\"3\"]}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"tool_version": "9.3+galaxy2",
"type": "tool",
"uuid": "b6796224-1789-45fd-8392-3237462c9071",
"when": null,
Expand Down Expand Up @@ -3876,7 +3945,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down
5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.3] 2024-08-19

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2`

## [0.2] 2024-08-12

### Added
Expand Down

0 comments on commit ae2cebc

Please sign in to comment.