From 9da128723be76f83269114b5b256bf86501ad896 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Thu, 15 Feb 2024 10:42:35 -0500 Subject: [PATCH] add histogram outputs to merqury --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 82 ++++++------------- .../CHANGELOG.md | 4 + 2 files changed, 30 insertions(+), 56 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga index 3be5db340d..30705c4918 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.2", + "release": "0.1.3", "name": "Assembly-Hifi-Trio-phasing-VGP5", "steps": { "0": { @@ -205,13 +205,7 @@ "type": "parameter_input", "uuid": "a5987ed3-6fdb-49c7-92d0-5b2f78a9bbb9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2cfefbef-173b-4bb1-944b-d66ecba6c40c" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -265,13 +259,7 @@ "type": "data_input", "uuid": "80ff22ac-1a58-4f89-bf52-48f18d8f71f9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a949a15c-bc4c-4002-bc94-f3b8d3d2861d" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -298,13 +286,7 @@ "type": "parameter_input", "uuid": "c5651e7e-31d4-41b7-a590-e2fadc7f59e9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "91a2700d-e617-49ed-9c5e-c285d2a0068b" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "", @@ -331,13 +313,7 @@ "type": "parameter_input", "uuid": "1ae103f4-38e9-4414-8e46-b8a763159937", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "5aa55234-4876-4dc4-8a26-0cff1283bb08" - } - ] + "workflow_outputs": [] }, "11": { "annotation": "", @@ -564,7 +540,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"blank\", \"__current_case__\": 0}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"trio\", \"__current_case__\": 1, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"trioinput\": {\"trio_input_selector\": \"reads\", \"__current_case__\": 0, \"hap1_reads\": {\"__class__\": \"RuntimeValue\"}, \"hap2_reads\": {\"__class__\": \"RuntimeValue\"}}, \"max_kmers\": \"2\", \"min_kmers\": \"5\", \"yak_kmer_length\": \"31\", \"trio_dual\": false}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"blank\", \"__current_case__\": 0}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"trio\", \"__current_case__\": 1, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"trioinput\": {\"trio_input_selector\": \"reads\", \"__current_case__\": 0, \"hap1_reads\": {\"__class__\": \"ConnectedValue\"}, \"hap2_reads\": {\"__class__\": \"ConnectedValue\"}}, \"max_kmers\": \"2\", \"min_kmers\": \"5\", \"yak_kmer_length\": \"31\", \"trio_dual\": false}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.19.8+galaxy0", "type": "tool", "uuid": "50aee4e7-5172-49a0-a448-4020942301af", @@ -681,7 +657,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.6+galaxy0", "type": "tool", "uuid": "ae31efe9-7f56-4a2d-b811-d77d4f8b0abf", @@ -754,7 +730,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.6+galaxy0", "type": "tool", "uuid": "f2a02b12-43b7-4969-a999-dbc18b820c2f", @@ -1321,15 +1297,15 @@ "uuid": "4931c626-b636-43c3-b19b-3c778199b9a8", "when": null, "workflow_outputs": [ - { - "label": "Busco Summary Image Hap2", - "output_name": "summary_image", - "uuid": "caf3c70a-11cf-468f-aab8-144a38880d07" - }, { "label": "Busco Summary Hap2", "output_name": "busco_sum", "uuid": "b1bae72f-2729-47d4-925c-ddbba82e2098" + }, + { + "label": "Busco Summary Image Hap2", + "output_name": "summary_image", + "uuid": "caf3c70a-11cf-468f-aab8-144a38880d07" } ] }, @@ -1401,6 +1377,10 @@ "name": "stats_files", "type": "input" }, + { + "name": "hist_files", + "type": "input" + }, { "name": "log_file", "type": "txt" @@ -1466,7 +1446,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"trio\", \"__current_case__\": 1, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"meryldb_PAT\": {\"__class__\": \"ConnectedValue\"}, \"meryldb_MAT\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}, \"assembly_02\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": true, \"output_selector\": [\"qv\", \"plots\", \"sizes\", \"stats\", \"bed\", \"wig\", \"log\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"trio\", \"__current_case__\": 1, \"meryldb_F1\": {\"__class__\": \"RuntimeValue\"}, \"meryldb_PAT\": {\"__class__\": \"RuntimeValue\"}, \"meryldb_MAT\": {\"__class__\": \"RuntimeValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"RuntimeValue\"}, \"assembly_02\": {\"__class__\": \"RuntimeValue\"}}}, \"output_add_headers\": true, \"output_selector\": [\"qv\", \"plots\", \"sizes\", \"stats\", \"bed\", \"wig\", \"log\", \"hist\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy3", "type": "tool", "uuid": "25a1c5c3-56b1-490a-b73e-ad8cd94c1c26", @@ -2906,25 +2886,15 @@ "uuid": "bc14963b-acf4-4064-ad92-fbf7cad3730f", "when": null, "workflow_outputs": [ - { - "label": "Nx Plot", - "output_name": "Nx Plot", - "uuid": "4235c91f-2071-483e-b905-bed50bc53b05" - }, - { - "label": null, - "output_name": "3:output", - "uuid": "f7e65b5f-a315-482e-910c-3d41279a3b59" - }, - { - "label": null, - "output_name": "2:output", - "uuid": "2530c4c5-5f68-48a4-9da1-c86696f84a1f" - }, { "label": "Size Plot", "output_name": "Size Plot", "uuid": "044f639b-f8f9-44b9-85b0-bbea417e4af7" + }, + { + "label": "Nx Plot", + "output_name": "Nx Plot", + "uuid": "4235c91f-2071-483e-b905-bed50bc53b05" } ] }, @@ -3270,6 +3240,6 @@ "VGP", "Reviewed" ], - "uuid": "0db51f45-52e7-4f61-a619-11af3d4f5219", - "version": 2 -} + "uuid": "cb7f8a94-71f3-48c3-9f7b-3cfb2ed86cb2", + "version": 1 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md index 639095cf86..fc67256d24 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md @@ -1,6 +1,10 @@ # Changelog +## [0.1.3] 2024-02-15 + +- Add histogram outputs to merqury + ## [0.1.2] 2023-11-14