Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4 #572

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4 #572

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
45 changes: 34 additions & 11 deletions workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
],
"format-version": "0.1",
"license": "BSD-3-Clause",
"release": "0.3",
"release": "0.4",
"name": "Assembly-decontamination-VGP9",
"report": {
"markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
Expand Down Expand Up @@ -88,7 +88,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool NCBI BLAST+ dustmasker",
"name": "db_opts"
}
],
"label": "soft-masking ",
"name": "NCBI BLAST+ dustmasker",
"outputs": [
Expand Down Expand Up @@ -167,7 +172,7 @@
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "5089350b-c1a9-498a-9786-9864d484f77a",
Expand All @@ -189,7 +194,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Kraken2",
"name": "single_paired"
}
],
"label": "ID non-target contaminants",
"name": "Kraken2",
"outputs": [
Expand Down Expand Up @@ -448,7 +458,7 @@
}
},
"tool_id": "Cut1",
"tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "8cc3e58f-2940-454a-9cf6-b32c1ab19016",
Expand Down Expand Up @@ -508,7 +518,7 @@
},
"11": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
"errors": null,
"id": 11,
"input_connections": {
Expand All @@ -521,7 +531,20 @@
"output_name": "out_file1"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
},
{
"description": "runtime parameter for tool gfastats",
"name": "target_condition"
},
{
"description": "runtime parameter for tool gfastats",
"name": "target_condition"
}
],
"label": "removing scaffolds ",
"name": "gfastats",
"outputs": [
Expand All @@ -535,15 +558,15 @@
"top": 798.078125
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
"tool_shed_repository": {
"changeset_revision": "3ef480892a9f",
"changeset_revision": "f4a3eff8ab85",
"name": "gfastats",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.3.6+galaxy0",
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.3.9+galaxy0",
"type": "tool",
"uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed",
"when": null,
Expand Down
5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.4] 2024-11-11

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0`

## [0.3] 2024-08-26

- Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes.
Expand Down
Loading