From 5872e431f7c6b6ab1b9e404c3c25e249c61477c0 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 12 Jul 2024 11:11:42 +0200 Subject: [PATCH 1/3] add workflow report --- .../kmer-profiling-hifi-VGP1/CHANGELOG.md | 4 +++ .../kmer-profiling-hifi-VGP1.ga | 36 ++++++++++--------- 2 files changed, 24 insertions(+), 16 deletions(-) diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index 261693f89..0b3001964 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.1.6] 2024-07-12 + +- Add workflow report + ## [0.1.5] 2023-11-20 - Fix author in dockstore diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index 238ddea7e..e268e7ee3 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "creator": [ { "class": "Organization", @@ -14,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release":"0.1.5", + "release":"0.1.6", "name": "kmer-profiling-hifi-VGP1", + "report": { + "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n```galaxy\nworkflow_image()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "A simple list collection containing PacBio data in either fastq or fasta format", @@ -33,7 +37,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 86.5078125 }, "tool_id": null, @@ -73,7 +77,7 @@ { "label": null, "output_name": "output", - "uuid": "18b69ad3-4c09-46f5-9a4c-bf4097b37fef" + "uuid": "a4240190-0161-4966-b3f0-9a19b27e11fe" } ] }, @@ -106,7 +110,7 @@ { "label": null, "output_name": "output", - "uuid": "1fea95fa-67d6-408d-94b6-264107cc19a1" + "uuid": "02e6daaf-94a2-4708-a932-abe0a450c10e" } ] }, @@ -377,6 +381,16 @@ "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, "workflow_outputs": [ + { + "label": "GenomeScope Model Parameters", + "output_name": "model_params", + "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" + }, + { + "label": "GenomeScope log plot", + "output_name": "log_plot", + "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" + }, { "label": "GenomeScope linear plot", "output_name": "linear_plot", @@ -396,16 +410,6 @@ "label": "GenomeScope summary", "output_name": "summary", "uuid": "b74004e1-4f4b-4f43-a9f0-2a7a0a70ca1d" - }, - { - "label": "GenomeScope Model Parameters", - "output_name": "model_params", - "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" - }, - { - "label": "GenomeScope log plot", - "output_name": "log_plot", - "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" } ] } @@ -414,6 +418,6 @@ "Reviewed", "VGP" ], - "uuid": "7542ffba-d083-415e-b745-08d9503debc4", - "version": 4 + "uuid": "253fec6a-351a-40b8-b602-19a305142e85", + "version": 1 } \ No newline at end of file From 5f156c112f10cda11c13aa88aa77c13565c50cab Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 12 Jul 2024 18:18:00 +0200 Subject: [PATCH 2/3] removed tab suspected to cause a linting problem --- .../kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index e268e7ee3..764131b0e 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release":"0.1.6", + "release":"0.1.6", "name": "kmer-profiling-hifi-VGP1", "report": { "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n```galaxy\nworkflow_image()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" From 839005f5d3b7fa1d7ce3eaf0a5ec299e05ca27b2 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 16 Jul 2024 16:23:40 -0400 Subject: [PATCH 3/3] remove display workflow as image from the report --- .../kmer-profiling-hifi-VGP1.ga | 42 +++++++------------ 1 file changed, 15 insertions(+), 27 deletions(-) diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index 764131b0e..b3a112c3b 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -18,7 +18,7 @@ "release":"0.1.6", "name": "kmer-profiling-hifi-VGP1", "report": { - "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n```galaxy\nworkflow_image()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, "steps": { "0": { @@ -73,13 +73,7 @@ "type": "parameter_input", "uuid": "946bcadd-8ab0-4595-9985-abb574539844", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a4240190-0161-4966-b3f0-9a19b27e11fe" - } - ] + "workflow_outputs": [] }, "2": { "annotation": "Ploidy for the organism being assembled", @@ -106,13 +100,7 @@ "type": "parameter_input", "uuid": "e3848560-55a2-42a5-ac1a-487ccf084d92", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "02e6daaf-94a2-4708-a932-abe0a450c10e" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "", @@ -381,16 +369,6 @@ "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, "workflow_outputs": [ - { - "label": "GenomeScope Model Parameters", - "output_name": "model_params", - "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" - }, - { - "label": "GenomeScope log plot", - "output_name": "log_plot", - "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" - }, { "label": "GenomeScope linear plot", "output_name": "linear_plot", @@ -410,6 +388,16 @@ "label": "GenomeScope summary", "output_name": "summary", "uuid": "b74004e1-4f4b-4f43-a9f0-2a7a0a70ca1d" + }, + { + "label": "GenomeScope Model Parameters", + "output_name": "model_params", + "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" + }, + { + "label": "GenomeScope log plot", + "output_name": "log_plot", + "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" } ] } @@ -418,6 +406,6 @@ "Reviewed", "VGP" ], - "uuid": "253fec6a-351a-40b8-b602-19a305142e85", - "version": 1 + "uuid": "0808b15a-7e3e-4b06-b804-f3d2cc73981a", + "version": 2 } \ No newline at end of file