diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md index 7e61eeab6a..e33835f1ef 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.10.5] - 2025-10-06 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2` + ## [0.10.4] - 2025-09-29 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga index 28bb4993bf..5a86628529 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga @@ -461,7 +461,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -513,7 +522,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -783,7 +797,16 @@ "output_name": "split_fasta" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1003,7 +1026,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1124,7 +1152,20 @@ "output_name": "alignment_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1186,7 +1227,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1298,7 +1348,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "errors": null, "id": 30, "input_connections": { @@ -1315,7 +1365,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": "Busco on purged primary/hap1 assembly", "name": "Busco", "outputs": [ @@ -1381,15 +1436,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "4e70d88adf2f", + "changeset_revision": "c5a90fa4b8dd", "name": "busco", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"cached_db\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"test\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.8.0+galaxy1", + "tool_version": "5.8.0+galaxy2", "type": "tool", "uuid": "88073363-2f5c-4486-a23a-1cfdc4f5e6a6", "when": null, @@ -1417,7 +1472,12 @@ "output_name": "get_seqs_purged" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1709,7 +1769,16 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1763,7 +1832,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2215,7 +2289,7 @@ } }, "tags": [], - "uuid": "ac02e560-9046-4b88-8b0a-b787e5e418f7" + "uuid": "12d667cc-e145-4961-84b5-be80c8799d2e" }, "tool_id": null, "type": "subworkflow", @@ -2242,7 +2316,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2366,7 +2445,16 @@ "output_name": "split_fasta" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -2428,7 +2516,20 @@ "output_name": "alignment_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2490,7 +2591,16 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2674,7 +2784,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2795,7 +2910,12 @@ "output_name": "get_seqs_purged" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2839,7 +2959,7 @@ }, "47": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "errors": null, "id": 47, "input_connections": { @@ -2856,7 +2976,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -2922,15 +3047,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "4e70d88adf2f", + "changeset_revision": "c5a90fa4b8dd", "name": "busco", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"cached_db\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"test\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.8.0+galaxy1", + "tool_version": "5.8.0+galaxy2", "type": "tool", "uuid": "2f798d45-e619-4a33-b4e9-c61912b7f956", "when": null, @@ -3502,7 +3627,7 @@ } }, "tags": [], - "uuid": "cebd48be-5426-4f47-b16b-d9e711b69bfe" + "uuid": "ccbbc122-4d34-45c0-969f-ca50bec18252" }, "tool_id": null, "type": "subworkflow", @@ -4333,7 +4458,7 @@ } }, "tags": [], - "uuid": "936aa0a5-2265-4505-bdd6-9a4c3beadeda" + "uuid": "383cf2e6-9895-4b72-8c47-64086a86c743" }, "tool_id": null, "type": "subworkflow", @@ -4467,7 +4592,7 @@ "tags": [ "VGP_curated" ], - "uuid": "c4a1ca2e-13a0-4d0b-bdec-d5bbac5b9a34", + "uuid": "29d17313-8c9b-49fb-8db1-e725678ad66f", "version": 1, - "release": "0.10.4" -} + "release": "0.10.5" +} \ No newline at end of file