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 887c387a5..7f75c6bf6 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 + +## [0.3.8] 2024-04-23 + +- Add Busco Gff output + ## [0.3.7] 2024-04-22 ### 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 a921c0435..a004fd2a2 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 @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.3.7", + "release": "0.3.8", "name": "Purge-duplicate-contigs-VGP6", "steps": { "0": { @@ -303,16 +303,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -364,12 +355,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -510,16 +496,7 @@ "output_name": "split_fasta" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -739,12 +716,7 @@ "output_name": "integer_param" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -834,15 +806,15 @@ "uuid": "97ce37f6-db2d-483c-abab-813827929e9b", "when": null, "workflow_outputs": [ - { - "label": "Cutoffs for primary assembly", - "output_name": "calcuts_cutoff", - "uuid": "d2c6d9bd-e28f-4ff1-ac7b-f9068e49a582" - }, { "label": "Read Coverage and cutoffs calculation on primary assembly : Histogram plot", "output_name": "hist", "uuid": "2e045d9d-99e4-457f-9cee-691616ed6590" + }, + { + "label": "Cutoffs for primary assembly", + "output_name": "calcuts_cutoff", + "uuid": "d2c6d9bd-e28f-4ff1-ac7b-f9068e49a582" } ] }, @@ -865,20 +837,7 @@ "output_name": "alignment_output" } }, - "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" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -940,16 +899,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - }, - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1081,12 +1031,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1105,6 +1050,10 @@ { "name": "summary_image", "type": "png" + }, + { + "name": "busco_gff", + "type": "gff3" } ], "position": { @@ -1112,6 +1061,13 @@ "top": 1520.5883525119295 }, "post_job_actions": { + "TagDatasetActionbusco_gff": { + "action_arguments": { + "tags": "busco_p1_gff,name:p1" + }, + "action_type": "TagDatasetAction", + "output_name": "busco_gff" + }, "TagDatasetActionbusco_missing": { "action_arguments": { "tags": "busco_p1_missing, #p1" @@ -1148,21 +1104,21 @@ "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, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "88073363-2f5c-4486-a23a-1cfdc4f5e6a6", "when": null, "workflow_outputs": [ - { - "label": "Busco on Purged Primary assembly: short summary", - "output_name": "busco_sum", - "uuid": "87515aeb-4e2e-494f-a271-44013d0944e4" - }, { "label": "Busco on Purged Primary assembly: summary image", "output_name": "summary_image", "uuid": "d1ecf9fe-3f76-465d-bcac-cf5b4986a8e8" + }, + { + "label": "Busco on Purged Primary assembly: short summary", + "output_name": "busco_sum", + "uuid": "87515aeb-4e2e-494f-a271-44013d0944e4" } ] }, @@ -1181,12 +1137,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1341,16 +1292,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1404,12 +1346,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1891,12 +1828,7 @@ "output_name": "integer_param" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1993,15 +1925,15 @@ "uuid": "0496de4b-ec62-48d5-8c36-e2f946ca728d", "when": null, "workflow_outputs": [ - { - "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot", - "output_name": "hist", - "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70" - }, { "label": "Cutoffs for alternate assembly", "output_name": "calcuts_cutoff", "uuid": "49bf0c95-0290-4f8b-a9d7-2f17f53e9d26" + }, + { + "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot", + "output_name": "hist", + "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70" } ] }, @@ -2020,16 +1952,7 @@ "output_name": "split_fasta" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -2091,20 +2014,7 @@ "output_name": "alignment_output" } }, - "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" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2166,16 +2076,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - }, - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2352,12 +2253,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -2399,6 +2295,13 @@ "action_type": "TagDatasetAction", "output_name": "bed_files" }, + "TagDatasetActionhist_files": { + "action_arguments": { + "tags": "merqury_p_hist,name:p" + }, + "action_type": "TagDatasetAction", + "output_name": "hist_files" + }, "TagDatasetActionpng_files": { "action_arguments": { "tags": "merqury_p_png, #p" @@ -2448,15 +2351,15 @@ "uuid": "133c60bc-4171-44b4-bf22-c70c623265b2", "when": null, "workflow_outputs": [ - { - "label": "Merqury on Phased assemblies: stats", - "output_name": "stats_files", - "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae" - }, { "label": "Merqury on Phased assemblies: Images", "output_name": "png_files", "uuid": "ff9cfc96-449e-41d8-9c10-7f586ab6f479" + }, + { + "label": "Merqury on Phased assemblies: stats", + "output_name": "stats_files", + "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae" } ] }, @@ -2475,12 +2378,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -3543,6 +3441,6 @@ "tags": [ "VGP_curated" ], - "uuid": "6b1b52f2-833c-4532-95c0-c85bc238fc76", - "version": 1 -} + "uuid": "4818fdda-7a91-481a-a62f-ccab45a3c0f1", + "version": 2 +} \ No newline at end of file