From 78bd3c0a87ecf2cdf806df2f9adb10e3086b0917 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 13 Aug 2024 15:00:19 -0400 Subject: [PATCH] expose busco parameter --- .../Assembly-Hifi-only-VGP3-tests.yml | 1 + .../Assembly-Hifi-only-VGP3.ga | 375 +++++++++--------- .../Assembly-Hifi-only-VGP3/CHANGELOG.md | 4 + .../Assembly-Hifi-only-VGP3/README.md | 33 +- 4 files changed, 203 insertions(+), 210 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index f8af1a040..f00fcbb5b 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -23,6 +23,7 @@ Bits for Hifiasm bloom filter: 32 SAK input file (Optional): null Homozygous Read Coverage: null + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 Name of primary assembly: Primary Name of alternate assembly: Alternate diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index 57d568faa..136b94576 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2", + "release": "0.2.1", "name": "Assembly-Hifi-only-VGP3", "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\n\n## BUSCO results (Vertebrata database)\n\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" @@ -127,13 +127,7 @@ "type": "parameter_input", "uuid": "3ce6ecc2-3262-4695-b4ef-1a58f52a48bd", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "66115e1f-5bbb-4d04-bf6a-5d4ed3dbd98b" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", @@ -160,13 +154,7 @@ "type": "parameter_input", "uuid": "1e16198c-a515-4b6d-9a72-d1de93974d2b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e3106a90-3aa4-45ab-9d2f-c813092abfa4" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", @@ -196,11 +184,38 @@ "workflow_outputs": [] }, "6": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "annotation": "", "content_id": null, "errors": null, "id": 6, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 422.96681360823476, + "top": 1352.5435082963184 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "af7ad6ad-2718-4a16-ad1f-6858b1b4fb50", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -211,8 +226,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 432.9672084074356, - "top": 1396.376653536473 + "left": 500.2702810213637, + "top": 1472.6772609095954 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -220,19 +235,13 @@ "type": "parameter_input", "uuid": "df030d72-fca9-4b7e-b58b-dcd27c453543", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "40afd0cd-399f-4e16-9980-09b69828ea06" - } - ] + "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -253,19 +262,13 @@ "type": "data_input", "uuid": "b7958e14-2495-4d38-8da1-ea583f5ae8e2", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "de381739-aacd-47a6-8520-0a5c4f5c9647" - } - ] + "workflow_outputs": [] }, - "8": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -286,19 +289,13 @@ "type": "parameter_input", "uuid": "163c033f-85ce-46e5-b00a-3b3904dea278", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2e8de303-a105-486c-b430-3f1cc34a91a5" - } - ] + "workflow_outputs": [] }, - "9": { + "10": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -319,19 +316,13 @@ "type": "parameter_input", "uuid": "88e40054-8605-4746-b91b-38ff85c70fd6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0abaae7b-0421-483d-bf25-a0efbae3e9f1" - } - ] + "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 10, + "id": 11, "input_connections": { "library|input_1": { "id": 0, @@ -387,11 +378,11 @@ "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 11, + "id": 12, "input_connections": { "infile": { "id": 2, @@ -432,11 +423,11 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 12, + "id": 13, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 3, @@ -471,11 +462,11 @@ "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", "errors": null, - "id": 13, + "id": 14, "input_connections": { "input": { "id": 5, @@ -516,14 +507,14 @@ "when": null, "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", "errors": null, - "id": 14, + "id": 15, "input_connections": { "results_0|software_cond|input": { - "id": 10, + "id": 11, "output_name": "report" } }, @@ -570,14 +561,14 @@ } ] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, - "id": 15, + "id": 16, "input_connections": { "infile": { - "id": 11, + "id": 12, "output_name": "output" } }, @@ -615,14 +606,14 @@ "when": null, "workflow_outputs": [] }, - "16": { + "17": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 16, + "id": 17, "input_connections": { "input": { - "id": 13, + "id": 14, "output_name": "out_file1" } }, @@ -654,14 +645,14 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "input": { - "id": 15, + "id": 16, "output_name": "outfile" } }, @@ -693,14 +684,14 @@ "when": null, "workflow_outputs": [] }, - "18": { + "19": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input1": { - "id": 16, + "id": 17, "output_name": "out_file1" } }, @@ -734,14 +725,14 @@ "when": null, "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input": { - "id": 17, + "id": 18, "output_name": "out_file1" } }, @@ -773,18 +764,18 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 20, + "id": 21, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 4, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 18, + "id": 19, "output_name": "integer_param" } }, @@ -824,14 +815,14 @@ "when": null, "workflow_outputs": [] }, - "21": { + "22": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 21, + "id": 22, "input_connections": { "input1": { - "id": 19, + "id": 20, "output_name": "out_file1" } }, @@ -878,22 +869,22 @@ } ] }, - "22": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, - "id": 22, + "id": 23, "input_connections": { "assembly_options|hom_cov": { - "id": 20, + "id": 21, "output_name": "integer_param" }, "filter_bits": { - "id": 12, + "id": 13, "output_name": "integer_param" }, "mode|reads": { - "id": 10, + "id": 11, "output_name": "out1" } }, @@ -992,14 +983,14 @@ } ] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4", "errors": null, - "id": 23, + "id": 24, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "raw_unitigs" } }, @@ -1045,18 +1036,18 @@ } ] }, - "24": { + "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "alternate_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1109,18 +1100,18 @@ } ] }, - "25": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 25, + "id": 26, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "primary_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1173,18 +1164,18 @@ } ] }, - "26": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "primary_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1244,18 +1235,18 @@ } ] }, - "27": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 27, + "id": 28, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "alternate_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1315,18 +1306,18 @@ } ] }, - "28": { + "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 28, + "id": 29, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "primary_contig_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 21, + "id": 22, "output_name": "integer_param" } }, @@ -1372,18 +1363,18 @@ } ] }, - "29": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "alternate_contig_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 21, + "id": 22, "output_name": "integer_param" } }, @@ -1429,14 +1420,14 @@ } ] }, - "30": { + "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 30, + "id": 31, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "primary_contig_graph" } }, @@ -1481,14 +1472,14 @@ "when": null, "workflow_outputs": [] }, - "31": { + "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 31, + "id": 32, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "alternate_contig_graph" } }, @@ -1533,19 +1524,23 @@ "when": null, "workflow_outputs": [] }, - "32": { + "33": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 32, + "id": 33, "input_connections": { "input": { - "id": 26, + "id": 27, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 6, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 7, + "output_name": "output" } }, "inputs": [], @@ -1621,7 +1616,7 @@ "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\", \"gff\"], \"__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\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", @@ -1634,18 +1629,18 @@ } ] }, - "33": { + "34": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4", "errors": null, - "id": 33, + "id": 34, "input_connections": { "mode|assembly_options|assembly_01": { - "id": 26, + "id": 27, "output_name": "output" }, "mode|assembly_options|assembly_02": { - "id": 27, + "id": 28, "output_name": "output" }, "mode|meryldb_F1": { @@ -1751,11 +1746,6 @@ "uuid": "da32529d-f84c-4af6-b443-eddfc1705d78", "when": null, "workflow_outputs": [ - { - "label": "Merqury png", - "output_name": "png_files", - "uuid": "1040586b-b0aa-41c3-98e4-00ead4e43a5c" - }, { "label": "Merqury Histograms", "output_name": "hist_files", @@ -1765,17 +1755,22 @@ "label": "Merqury completeness stats", "output_name": "stats_files", "uuid": "640107ca-7175-4624-9851-33911c197b18" + }, + { + "label": "Merqury png", + "output_name": "png_files", + "uuid": "1040586b-b0aa-41c3-98e4-00ead4e43a5c" } ] }, - "34": { + "35": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 34, + "id": 35, "input_connections": { "infile": { - "id": 28, + "id": 29, "output_name": "stats" } }, @@ -1813,14 +1808,14 @@ "when": null, "workflow_outputs": [] }, - "35": { + "36": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 35, + "id": 36, "input_connections": { "infile": { - "id": 29, + "id": 30, "output_name": "stats" } }, @@ -1858,12 +1853,12 @@ "when": null, "workflow_outputs": [] }, - "36": { + "37": { "annotation": "", - "id": 36, + "id": 37, "input_connections": { "gfa_stats": { - "id": 30, + "id": 31, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -2240,12 +2235,12 @@ "when": null, "workflow_outputs": [] }, - "37": { + "38": { "annotation": "", - "id": 37, + "id": 38, "input_connections": { "gfa_stats": { - "id": 31, + "id": 32, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -2622,14 +2617,14 @@ "when": null, "workflow_outputs": [] }, - "38": { + "39": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 38, + "id": 39, "input_connections": { "input": { - "id": 33, + "id": 34, "output_name": "qv_files" } }, @@ -2667,14 +2662,14 @@ } ] }, - "39": { + "40": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 39, + "id": 40, "input_connections": { "input": { - "id": 33, + "id": 34, "output_name": "png_files" } }, @@ -2712,14 +2707,14 @@ } ] }, - "40": { + "41": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 40, + "id": 41, "input_connections": { "input": { - "id": 33, + "id": 34, "output_name": "png_files" } }, @@ -2757,14 +2752,14 @@ } ] }, - "41": { + "42": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 41, + "id": 42, "input_connections": { "input": { - "id": 33, + "id": 34, "output_name": "png_files" } }, @@ -2802,14 +2797,14 @@ } ] }, - "42": { + "43": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 42, + "id": 43, "input_connections": { "input": { - "id": 33, + "id": 34, "output_name": "stats_files" } }, @@ -2847,18 +2842,18 @@ } ] }, - "43": { + "44": { "annotation": "", "content_id": "join1", "errors": null, - "id": 43, + "id": 44, "input_connections": { "input1": { - "id": 34, + "id": 35, "output_name": "outfile" }, "input2": { - "id": 35, + "id": 36, "output_name": "outfile" } }, @@ -2884,27 +2879,27 @@ "when": null, "workflow_outputs": [] }, - "44": { + "45": { "annotation": "", - "id": 44, + "id": 45, "input_connections": { "Alternate data": { - "id": 37, + "id": 38, "input_subworkflow_step_id": 1, "output_name": "gfastats data for plotting" }, "Name of alternate assembly": { - "id": 9, + "id": 10, "input_subworkflow_step_id": 3, "output_name": "output" }, "Name of primary assembly": { - "id": 8, + "id": 9, "input_subworkflow_step_id": 2, "output_name": "output" }, "Primary data": { - "id": 36, + "id": 37, "input_subworkflow_step_id": 0, "output_name": "gfastats data for plotting" } @@ -3416,35 +3411,25 @@ "when": null, "workflow_outputs": [ { - 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"46": { + "47": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 46, + "id": 47, "input_connections": { "infile": { - "id": 45, + "id": 46, "output_name": "output" } }, @@ -3553,6 +3538,6 @@ "VGP", "Reviewed" ], - "uuid": "39c93c40-5bcb-42f2-a12e-a4a4fae21ed7", - "version": 12 + "uuid": "2988562a-fa7a-4135-bf67-943ab03d1517", + "version": 1 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md index 38064d35b..cac117d0b 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.2.1] 2024-08-13 + +- Expose Busco lineage database parameter + ## [0.2] 2024-08-01 ### Added diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md index 47180d7c5..8d24d78ca 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md @@ -1,26 +1,29 @@ -## Contiging Solo w/HiC: +## Contiging Solo: -Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing. +Generate assembly based on PacBio Hifi Reads. ### Inputs 1. Hifi long reads [fastq] -2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq] -3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq] -4. K-mer database [meryldb] -5. Genome profile summary generated by Genomescope [txt] -6. Name of first assembly -7. Name of second assembly +2. K-mer database [meryldb] +3. Genome profile summary generated by Genomescope [txt] +4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate. +5. Genomescope Model Parameters generated by Genomescope [tabular] +6. Database for busco lineage (recommended: latest) +7. Busco lineage (recommended: vertebrata) +8. Name of first assembly +9. Name of second assembly ### Outputs -1. Haplotype 1 assembly -2. Haplotype 2 assembly -3. QC: BUSCO report for both assemblies -4. QC: Merqury report for both assemblies -5. QC: Assembly statistics for both assemblies -6. QC: Nx plot for both assemblies -7. QC: Size plot for both assemblie +1. Primary assembly +2. Alternate assembly +3. QC: Bandage image for the raw unitigs +4. QC: BUSCO report for both assemblies +5. QC: Merqury report for both assemblies +6. QC: Assembly statistics for both assemblies +7. QC: Nx plot for both assemblies +8. QC: Size plot for both assemblie