From b79258def177da757a0ccec3f968c940900269c1 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 12 Jul 2024 18:07:27 +0200 Subject: [PATCH 1/5] add workflow report and fix bug in joining assembly statistics --- .../Assembly-Hifi-HiC-phasing-VGP4-tests.yml | 4 +- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 546 +++++++++++++++--- .../CHANGELOG.md | 11 + 3 files changed, 493 insertions(+), 68 deletions(-) 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..ea66714af 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": "0.1.12", "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_display(output=\"Assembly statistics for Hap1 and Hap2\")\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.", @@ -183,7 +186,13 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "a7c8f776-78b1-4caa-b63f-f2cb96c9308b" + } + ] }, "6": { "annotation": "", @@ -210,7 +219,13 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d130c749-1851-491e-83a2-794f3ca263a1" + } + ] }, "7": { "annotation": "", @@ -237,7 +252,13 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "63859139-a7ef-4b30-a6a3-6b849b90d650" + } + ] }, "8": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", @@ -264,7 +285,13 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "81580b69-a114-4351-b9ae-b64f2ecc930c" + } + ] }, "9": { "annotation": "", @@ -291,7 +318,13 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c191eaba-164b-424c-949b-a0582810d785" + } + ] }, "10": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", @@ -318,7 +351,13 @@ "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "fe00ec3a-b6cd-4b28-ac33-98fd7c119b75" + } + ] }, "11": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", @@ -358,7 +397,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -898,7 +942,24 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "hic_partition" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "hic_partition" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": null, "name": "Hifiasm", "outputs": [ @@ -932,8 +993,8 @@ } ], "position": { - "left": 1419.8172582057985, - "top": 592 + "left": 1419.8124789715225, + "top": 592.1739029297412 }, "post_job_actions": { "HideDatasetActionhic_acontig_graph": { @@ -1041,7 +1102,13 @@ "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": "", @@ -1224,7 +1291,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1338,7 +1410,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1402,7 +1479,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1451,7 +1533,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1551,8 +1638,8 @@ } ], "position": { - "left": 2309.8172673668682, - "top": 423 + "left": 2016.52734375, + "top": 405.10546875 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1948,7 +2035,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "5c1cf1d2-ddbe-4427-bafd-3d44650729a1" }, "tool_id": null, @@ -2330,7 +2417,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "a1de3578-2b99-45a2-b972-8f199c863507" }, "tool_id": null, @@ -2461,18 +2548,31 @@ }, "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": [], + "inputs": [ + { + "description": "runtime parameter for tool Join two Datasets", + "name": "input1" + }, + { + "description": "runtime parameter for tool Join two Datasets", + "name": "input2" + } + ], "label": null, - "name": "Cut", + "name": "Join two Datasets", "outputs": [ { "name": "out_file1", @@ -2480,8 +2580,8 @@ } ], "position": { - "left": 2309.8172673668682, - "top": 233 + "left": 2369.40625, + "top": 424.50390625 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2490,11 +2590,11 @@ "output_name": "out_file1" } }, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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null, + "output_name": "3:output", + "uuid": "58904682-a049-4844-a9a9-fa3a83e67415" + }, + { + "label": null, + "output_name": "2:output", + "uuid": "997a0a2c-a9f4-47b0-b096-be9f4617ec91" + }, { "label": "Size Plot", "output_name": "Size Plot", @@ -3056,7 +3166,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -3082,8 +3197,8 @@ } ], "position": { - "left": 2311.5897610215297, - "top": 862.314072651286 + "left": 2309.3650867549095, + "top": 867.7323590806311 }, "post_job_actions": { "TagDatasetActionbusco_gff": { @@ -3135,6 +3250,11 @@ "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, "workflow_outputs": [ + { + "label": "Busco Summary Hap2", + "output_name": "busco_sum", + "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" + }, { "label": "Busco Gff File - Hap2", "output_name": "busco_gff", @@ -3144,11 +3264,6 @@ "label": "Busco Summary Image Hap2", "output_name": "summary_image", "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" - }, - { - "label": "Busco Summary Hap2", - "output_name": "busco_sum", - "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" } ] }, @@ -3171,7 +3286,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -3197,8 +3317,8 @@ } ], "position": { - "left": 2322.203125, - "top": 1392.99609375 + "left": 2307.6406963824797, + "top": 1460.0825909225844 }, "post_job_actions": { "HideDatasetActionlog_file": { @@ -3269,6 +3389,16 @@ "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, "workflow_outputs": [ + { + "label": "Merqury QV", + "output_name": "qv_files", + "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" + }, + { + "label": "Merqury Stats", + "output_name": "stats_files", + "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" + }, { "label": "Merqury 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"type": "tool", + "uuid": "c7ad672f-341b-4f2a-a5d2-b5ba9771cfef", + "when": null, + "workflow_outputs": [ + { + "label": "merqury_stats", + "output_name": "output", + "uuid": "b560b501-ef22-48f4-abbb-acbf793dfda1" + } + ] + }, + "50": { + "annotation": "", + "content_id": "__EXTRACT_DATASET__", + "errors": null, + "id": 50, + "input_connections": { + "input": { + "id": 42, + "output_name": "png_files" + } + }, + "inputs": [], + "label": "output_merqury.assembly_02.spectra-cn.fl", + "name": "Extract dataset", + "outputs": [ + { + "name": "output", + "type": "data" + } + ], + "position": { + "left": 2604.3436628906275, + "top": 2249.78125 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__EXTRACT_DATASET__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.assembly_02.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.1", + "type": "tool", + "uuid": "75f49e14-af85-4a07-81f1-3b75f591f965", + "when": null, + "workflow_outputs": [ + { + "label": "output_merqury.assembly_02.spectra-cn.fl", + "output_name": "output", + "uuid": "c10c5102-6b26-4cdc-bc35-50af09e36d9d" } ] } @@ -3448,6 +3862,6 @@ "VGP", "Reviewed" ], - "uuid": "cf273c22-e0eb-4a5f-8248-4a5d5102db1c", - "version": 1 -} + "uuid": "a128697a-2106-483f-9bbd-67b78c21b832", + "version": 24 +} \ 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..87be3e5ce 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 +## [0.1.12] 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 From c4d8dfd243494721a3ad75b58d148ea057deab61 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 12 Jul 2024 18:13:06 +0200 Subject: [PATCH 2/5] remove runtime parameters --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 86 +++---------------- 1 file changed, 10 insertions(+), 76 deletions(-) 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 ea66714af..311ad01fc 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 @@ -397,12 +397,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -942,24 +937,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hifiasm", - "name": "assembly_options" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "hic_partition" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "hic_partition" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Hifiasm", "outputs": [ @@ -1291,12 +1269,7 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1410,12 +1383,7 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1479,12 +1447,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1533,12 +1496,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -2561,16 +2519,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Join two Datasets", - "name": "input1" - }, - { - "description": "runtime parameter for tool Join two Datasets", - "name": "input2" - } - ], + "inputs": [], "label": null, "name": "Join two Datasets", "outputs": [ @@ -3166,12 +3115,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -3286,12 +3230,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -3426,12 +3365,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ From 62c4fcb3790ed2383901130c664679e8fa223798 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 16 Jul 2024 16:27:41 -0400 Subject: [PATCH 3/5] change tab to space that is causing linting error --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 311ad01fc..995e83fa9 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 @@ -20,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.12", + "release": "0.1.12", "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_display(output=\"Assembly statistics for Hap1 and Hap2\")\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" From 0f0a644852683793123bf4fdcd8e9e82b0995eb6 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Thu, 18 Jul 2024 12:55:10 -0400 Subject: [PATCH 4/5] replace character in statistic table that was causing problems in the report --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 179 +++++++++--------- 1 file changed, 92 insertions(+), 87 deletions(-) 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 995e83fa9..d791f7129 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 @@ -23,7 +23,7 @@ "release": "0.1.12", "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_display(output=\"Assembly statistics for Hap1 and Hap2\")\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" + "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": { @@ -186,13 +186,7 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a7c8f776-78b1-4caa-b63f-f2cb96c9308b" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "", @@ -219,13 +213,7 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "d130c749-1851-491e-83a2-794f3ca263a1" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -252,13 +240,7 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "63859139-a7ef-4b30-a6a3-6b849b90d650" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", @@ -285,13 +267,7 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "81580b69-a114-4351-b9ae-b64f2ecc930c" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -318,13 +294,7 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c191eaba-164b-424c-949b-a0582810d785" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", @@ -351,13 +321,7 @@ "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "fe00ec3a-b6cd-4b28-ac33-98fd7c119b75" - } - ] + "workflow_outputs": [] }, "11": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", @@ -1666,7 +1630,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 189.90056800842285 }, "tool_id": null, @@ -1699,7 +1663,7 @@ ], "position": { "left": 302.6136245727539, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2048,7 +2012,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 189.90056800842285 }, "tool_id": null, @@ -2081,7 +2045,7 @@ ], "position": { "left": 302.6136245727539, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -2540,7 +2504,7 @@ } }, "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__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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": "00e95547-9451-4c37-bc19-b29de3864c6a", @@ -2620,8 +2584,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, - "top": 0.0 + "left": 0, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -3078,25 +3042,15 @@ "uuid": "1b8e2d4e-3380-4414-bdb0-b356383c0ee2", "when": null, "workflow_outputs": [ - { - "label": "Nx Plot", - "output_name": "Nx Plot", - "uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4" - }, - { - "label": null, - "output_name": "3:output", - "uuid": "58904682-a049-4844-a9a9-fa3a83e67415" - }, - { - "label": null, - "output_name": "2:output", - "uuid": "997a0a2c-a9f4-47b0-b096-be9f4617ec91" - }, { "label": "Size Plot", "output_name": "Size Plot", "uuid": "03a0d2a8-c2d5-4ca7-80fe-7d04d1c4894a" + }, + { + "label": "Nx Plot", + "output_name": "Nx Plot", + "uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4" } ] }, @@ -3194,6 +3148,11 @@ "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, "workflow_outputs": [ + { + "label": "Busco Summary Image Hap2", + "output_name": "summary_image", + "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" + }, { "label": "Busco Summary Hap2", "output_name": "busco_sum", @@ -3203,11 +3162,6 @@ "label": "Busco Gff File - Hap2", "output_name": "busco_gff", "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" - }, - { - "label": "Busco Summary Image Hap2", - "output_name": "summary_image", - "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" } ] }, @@ -3328,16 +3282,6 @@ "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, "workflow_outputs": [ - { - "label": "Merqury QV", - "output_name": "qv_files", - "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" - }, - { - "label": "Merqury Stats", - "output_name": "stats_files", - "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" - }, { "label": "Merqury images", "output_name": "png_files", @@ -3347,6 +3291,16 @@ "label": "Merqury Histograms", "output_name": "hist_files", "uuid": "67d9d45d-989d-43c0-9ebd-0da9cc35763a" + }, + { + "label": "Merqury QV", + "output_name": "qv_files", + "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" + }, + { + "label": "Merqury Stats", + "output_name": "stats_files", + "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" } ] }, @@ -3449,15 +3403,15 @@ "output_name": "summary_image", "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" }, - { - "label": "Busco Summary Hap1", - "output_name": "busco_sum", - "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" - }, { "label": "Busco Gff File - Hap1", "output_name": "busco_gff", "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" + }, + { + "label": "Busco Summary Hap1", + "output_name": "busco_sum", + "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" } ] }, @@ -3790,12 +3744,63 @@ "uuid": "c10c5102-6b26-4cdc-bc35-50af09e36d9d" } ] + }, + "51": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 51, + "input_connections": { + "infile": { + "id": 44, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 2973.2736415223585, + "top": 446.09145245110693 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "fbf99087e067", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "7528118f-3c8c-47a8-86e8-6085145c38d1", + "when": null, + "workflow_outputs": [ + { + "label": "clean_stats", + "output_name": "outfile", + "uuid": "0d69a8ab-29c1-4fef-97d9-af243ca8eb83" + } + ] } }, "tags": [ "VGP", "Reviewed" ], - "uuid": "a128697a-2106-483f-9bbd-67b78c21b832", - "version": 24 + "uuid": "4135d455-ac66-4d86-b4a3-643580ff877f", + "version": 5 } \ No newline at end of file From 977d9a29f8f3286f526906a0ddafe52168de8635 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 23 Jul 2024 10:46:50 -0400 Subject: [PATCH 5/5] Apply suggestions from code review - Change release number Co-authored-by: Marius van den Beek --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 2 +- .../VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 d791f7129..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 @@ -20,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.12", + "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" 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 87be3e5ce..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 @@ -1,6 +1,6 @@ # Changelog -## [0.1.12] 2024-07-12 +## [0.2] 2024-07-12 ### Added