diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml index 55e219914..68205c04a 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml @@ -51,7 +51,7 @@ assert: has_n_line: n: 173 - Assembly statistics fir Hap1 and Hap2: + Assembly statistics for Hap1 and Hap2: asserts: has_text: - text: "Metric hap1 hap2" + text: "# scaffolds 72 35" diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index f8d827bf4..ff5d70639 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,8 +20,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.11", + "release": "0.2", "name": "Assembly-Hifi-HiC-phasing-VGP4", + "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_qv\")\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\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\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": { "0": { "annotation": "A simple list containing PacBio data in either fasta or fastq formats.", @@ -932,8 +935,8 @@ } ], "position": { - "left": 1419.8172582057985, - "top": 592 + "left": 1419.8124789715225, + "top": 592.1739029297412 }, "post_job_actions": { "HideDatasetActionhic_acontig_graph": { @@ -1041,7 +1044,13 @@ "type": "tool", "uuid": "c023af81-3c79-43f9-96df-8d982b19e4ed", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "raw unitig graph image", + "output_name": "outfile", + "uuid": "973f1ee3-d67f-4126-b9c0-301c9b0be6e7" + } + ] }, "25": { "annotation": "", @@ -1551,8 +1560,8 @@ } ], "position": { - "left": 2309.8172673668682, - "top": 423 + "left": 2016.52734375, + "top": 405.10546875 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1621,7 +1630,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 189.90056800842285 }, "tool_id": null, @@ -1654,7 +1663,7 @@ ], "position": { "left": 302.6136245727539, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -1948,7 +1957,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "5c1cf1d2-ddbe-4427-bafd-3d44650729a1" }, "tool_id": null, @@ -2003,7 +2012,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 189.90056800842285 }, "tool_id": null, @@ -2036,7 +2045,7 @@ ], "position": { "left": 302.6136245727539, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2330,7 +2339,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "a1de3578-2b99-45a2-b972-8f199c863507" }, "tool_id": null, @@ -2461,18 +2470,22 @@ }, "39": { "annotation": "", - "content_id": "Cut1", + "content_id": "join1", "errors": null, "id": 39, "input_connections": { - "input": { + "input1": { + "id": 34, + "output_name": "outfile" + }, + "input2": { "id": 33, "output_name": "outfile" } }, "inputs": [], "label": null, - "name": "Cut", + "name": "Join two Datasets", "outputs": [ { "name": "out_file1", @@ -2480,8 +2493,8 @@ } ], "position": { - "left": 2309.8172673668682, - "top": 233 + "left": 2369.40625, + "top": 424.50390625 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2490,11 +2503,11 @@ "output_name": "out_file1" } }, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.2", + "tool_id": "join1", + "tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"fill_empty\", \"__current_case__\": 1, \"fill_columns_by\": \"fill_unjoined_only\", \"do_fill_empty_columns\": {\"column_fill_type\": \"single_fill_value\", \"__current_case__\": 0, \"fill_value\": \".\"}}, \"header\": \"\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.1.3", "type": "tool", - "uuid": "1164d973-2ba9-4242-bae1-2a7b6c4678b6", + "uuid": "00e95547-9451-4c37-bc19-b29de3864c6a", "when": null, 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"tool", - "uuid": "bd181af5-44c6-4041-a2f0-e5cb8991b9fb", + "uuid": "7528118f-3c8c-47a8-86e8-6085145c38d1", "when": null, "workflow_outputs": [ { - "label": "Assembly statistics fir Hap1 and Hap2", - "output_name": "out_file1", - "uuid": "e83786b6-dd5e-4c91-8c36-c2d5eecab79d" + "label": "clean_stats", + "output_name": "outfile", + "uuid": "0d69a8ab-29c1-4fef-97d9-af243ca8eb83" } ] } @@ -3448,6 +3801,6 @@ "VGP", "Reviewed" ], - "uuid": "cf273c22-e0eb-4a5f-8248-4a5d5102db1c", - "version": 1 -} + "uuid": "4135d455-ac66-4d86-b4a3-643580ff877f", + "version": 5 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index a67f38ae6..4e6878d79 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.2] 2024-07-12 + +### Added + +- Workflow report + +### Changed + +- Fix bug where the columns of the assembly statistics didn't join properly. + + ## [0.1.11] 2024-05-20 ### Automatic update