From d74e8523dd9807ff4695638b75125e05cb80a99e Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Thu, 26 Oct 2023 16:00:33 -0400 Subject: [PATCH] add changes from Anton and exposed the busco lineage parameter --- .../Scaffolding-HiC-VGP8/CHANGELOG.md | 5 + .../Scaffolding-HiC-VGP8-tests.yml | 4 + .../Scaffolding-HiC-VGP8.ga | 508 ++++++++++-------- 3 files changed, 297 insertions(+), 220 deletions(-) diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index 262abaabb..005f10b16 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] + +## [0.1.1] - 2023-10-26 + +Added tags for better visibility of outputs in the history, and exposure of the BUSCO lineage parameter + ## [0.1] - 2023-09-27 Creation of the workflow and tests diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml index 5ef20a337..1bfec94c2 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml @@ -16,7 +16,10 @@ class: File location: https://zenodo.org/records/10037496/files/Estimated%20genome%20size%20-%20Parameter%20File.txt?download=1 filetype: txt + Sequence graph (optional): null Restriction enzymes: arima2 + Provide lineage for BUSCO (e.g., Vertebrata): vertebrata_odb10 + SAK input file (Optional): null outputs: Reconciliated scaffolds: asserts: @@ -44,3 +47,4 @@ asserts: has_line: line: "# scaffolds 84" + diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index d35e83800..82601ccc3 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "Scaffolding using HiC data with YAHS.", + "annotation": "", "creator": [ { "class": "Organization", @@ -13,8 +13,8 @@ } ], "format-version": "0.1", - "release": "0.1", "license": "CC-BY-4.0", + "release": "0.1.1", "name": "Scaffolding-HiC-VGP8", "steps": { "0": { @@ -34,13 +34,13 @@ "outputs": [], "position": { "left": 0, - "top": 189.0222684334385 + "top": 218.015625 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "aeb2045f-fa2e-4889-8420-3c10a544a436", + "uuid": "48622cc7-df63-4c71-8a1c-f0d2d326504d", "when": null, "workflow_outputs": [] }, @@ -53,21 +53,21 @@ "inputs": [ { "description": "", - "name": "Sequence graph" + "name": "Sequence graph (optional)" } ], - "label": "Sequence graph", + "label": "Sequence graph (optional)", "name": "Input dataset", "outputs": [], "position": { - "left": 335.39549974558594, - "top": 477.96875 + "left": 36.390625, + "top": 392.96875 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - 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