diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/.dockstore.yml b/workflows/VGP-assembly-v2/VGP-meryldb-creation/.dockstore.yml deleted file mode 100644 index 3a4b6aebc..000000000 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation/.dockstore.yml +++ /dev/null @@ -1,8 +0,0 @@ -version: 1.2 -workflows: -- name: main - primaryDescriptorPath: /meryldb-creation.ga - subclass: Galaxy - testParameterFiles: - - /meryldb-creation-tests.yml - publish: true diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/.dockstore.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/.dockstore.yml new file mode 100644 index 000000000..871d29318 --- /dev/null +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/.dockstore.yml @@ -0,0 +1,5 @@ +version: 1.2 +workflows: +- name: main + primaryDescriptorPath: /kmer-profiling-hifi-VGP1.ga + subclass: Galaxy diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/.workflowhub.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/.workflowhub.yml similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/.workflowhub.yml rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/.workflowhub.yml diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md similarity index 68% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/CHANGELOG.md rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index aa79d8016..8901188dd 100644 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -6,7 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] - +## [0.1.1] - 2023-10-30 +### Changed +- Names of the workflow and viles for consistency with other VGP workflows +- Labels and tags for user readability + ## [0.1] - 2021-08-26 ### Added - First version of the workflow. diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/README.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/README.md similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/README.md rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/README.md diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/meryldb-creation-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-test.ga similarity index 81% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/meryldb-creation-tests.yml rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-test.ga index 394928838..7c28a630e 100644 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation/meryldb-creation-tests.yml +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-test.ga @@ -1,4 +1,4 @@ -- doc: Test outline for meryldb-creation.ga +- doc: Test outline for kmer-profiling-hifi-VGP1.ga job: Collection of Pacbio Data: class: Collection @@ -31,19 +31,13 @@ file: test-data/GenomeScope_Transformed_log_plot.png compare: sim_size delta: 10000 - GenomeScope model: - asserts: - has_text: - text: 'Residual standard error: 577.3 on 159 degrees of freedom' - has_text: - text: 'Number of iterations to convergence: 18' GenomeScope summary: asserts: has_text: text: '27,842 bp' has_text: text: '35,913 bp' - GenomeScope model parameters: + GenomeScope Model Parameters: asserts: has_text: text: '0.0918418396430493' diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/meryldb-creation.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga similarity index 68% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/meryldb-creation.ga rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index 5770836b3..47930adc2 100644 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation/meryldb-creation.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.", + "annotation": "", "creator": [ { "class": "Organization", @@ -12,20 +12,20 @@ "name": "Galaxy" } ], - "release": "0.1", "format-version": "0.1", "license": "CC-BY-4.0", - "name": "Quality Evaluation", + "release": "0.1.1", + "name": "kmer-profiling-hifi-VGP1", "steps": { "0": { - "annotation": "Collection of Pacbio Data in fastq format.", + "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Collection of Pacbio Data in fastq format.", + "description": "", "name": "Collection of Pacbio Data" } ], @@ -33,31 +33,26 @@ "name": "Input dataset collection", "outputs": [], "position": { - "bottom": 274.671875, - "height": 82.171875, - "left": 158.5, - "right": 358.5, - "top": 192.5, - "width": 200, - "x": 158.5, - "y": 192.5 + "left": 25.07814953674619, + "top": 0 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "bcd448e1-e3d2-4764-8c27-422874b93ff2", + "uuid": "861c3a49-1055-4030-9a91-e53cbf1ac436", + "when": null, "workflow_outputs": [] }, "1": { - "annotation": "K-mer length used to calculate k-mer spectra. For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).", + "annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "K-mer length used to calculate k-mer spectra. For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).", + "description": "", "name": "K-mer length " } ], @@ -65,31 +60,26 @@ "name": "Input parameter", "outputs": [], "position": { - "bottom": 470.28125, - "height": 61.78125, - "left": 158.5, - "right": 358.5, - "top": 408.5, - "width": 200, - "x": 158.5, - "y": 408.5 + "left": 0, + "top": 290.01566057828205 }, "tool_id": null, "tool_state": "{\"default\": 21, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", - "uuid": "e3b1a943-df35-4271-aad8-49c1ed78e139", + "uuid": "946bcadd-8ab0-4595-9985-abb574539844", + "when": null, "workflow_outputs": [] }, "2": { - "annotation": "Ploidy for model to use. Default=2", + "annotation": "", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Ploidy for model to use. Default=2", + "description": "", "name": "Ploidy" } ], @@ -97,25 +87,20 @@ "name": "Input parameter", "outputs": [], "position": { - "bottom": 430.28125, - "height": 61.78125, - "left": 991.828125, - "right": 1191.828125, - "top": 368.5, - "width": 200, - "x": 991.828125, - "y": 368.5 + "left": 16.37496564855541, + "top": 493.99999877316264 }, "tool_id": null, "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", - "uuid": "8f5a1050-c9ec-4882-a9d4-d879fe7e9b20", + "uuid": "e3848560-55a2-42a5-ac1a-487ccf084d92", + "when": null, "workflow_outputs": [] }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, "id": 3, "input_connections": { @@ -138,14 +123,8 @@ } ], "position": { - "bottom": 325.453125, - "height": 143.953125, - "left": 436.28125, - "right": 636.28125, - "top": 181.5, - "width": 200, - "x": 436.28125, - "y": 181.5 + "left": 326.0155759265076, + "top": 0.9843835878612026 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -154,22 +133,23 @@ "output_name": "read_db" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "tool_shed_repository": { - "changeset_revision": "9cd178127b19", + "changeset_revision": "29dabd8db6f2", "name": "meryl", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy5", + "tool_version": "1.3+galaxy6", "type": "tool", - "uuid": "46f024d1-f0ee-4fdd-aea8-061e434c8326", + "uuid": "9f3718fe-c33a-43c1-b36e-964a929678f7", + "when": null, "workflow_outputs": [] }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, "id": 4, "input_connections": { @@ -188,46 +168,41 @@ } ], "position": { - "bottom": 320.0625, - "height": 113.5625, - "left": 714.0625, - "right": 914.0625, - "top": 206.5, - "width": 200, - "x": 714.0625, - "y": 206.5 + "left": 594.7968602779522, + "top": 127.82813604153586 }, "post_job_actions": { "TagDatasetActionread_db": { "action_arguments": { - "tags": "meryl_db" + "tags": "meryl_db,Meryl Database" }, "action_type": "TagDatasetAction", "output_name": "read_db" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "tool_shed_repository": { - "changeset_revision": "9cd178127b19", + "changeset_revision": "29dabd8db6f2", "name": "meryl", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"operation_type\": {\"command_type\": \"groups-kmers\", \"__current_case__\": 3, \"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy5", + "tool_version": "1.3+galaxy6", "type": "tool", - "uuid": "d5bcfdeb-0c22-4a42-a98d-f201cddbbf0e", + "uuid": "6467a6da-23e0-4ee0-af0e-7f5fc8a636de", + "when": null, "workflow_outputs": [ { "label": "Merged Meryl Database", "output_name": "read_db", - "uuid": "8284e7bd-3cd4-46a7-9952-ce6a76bc1078" + "uuid": "9055fdc0-d158-435e-b662-e5a4f2766b42" } ] }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, "id": 5, "input_connections": { @@ -246,14 +221,8 @@ } ], "position": { - "bottom": 310.0625, - "height": 113.5625, - "left": 991.828125, - "right": 1191.828125, - "top": 196.5, - "width": 200, - "x": 991.828125, - "y": 196.5 + "left": 884.453149536746, + "top": 76.92187131948805 }, "post_job_actions": { "HideDatasetActionread_db_hist": { @@ -262,17 +231,18 @@ "output_name": "read_db_hist" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "tool_shed_repository": { - "changeset_revision": "9cd178127b19", + "changeset_revision": "29dabd8db6f2", "name": "meryl", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy5", + "tool_version": "1.3+galaxy6", "type": "tool", - "uuid": "73e1c147-700d-4707-9a93-fd2ba8b2a32f", + "uuid": "10eb771d-1437-4602-91b7-e7e6d806dc2e", + "when": null, "workflow_outputs": [] }, "6": { @@ -294,12 +264,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool GenomeScope", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "GenomeScope", "outputs": [ @@ -333,26 +298,20 @@ } ], "position": { - "bottom": 756.703125, - "height": 540.203125, - "left": 1279.609375, - "right": 1479.609375, - "top": 216.5, - "width": 200, - "x": 1279.609375, - "y": 216.5 + "left": 1172.0166187911489, + "top": 96.88919830322266 }, "post_job_actions": { "TagDatasetActionlinear_plot": { "action_arguments": { - "tags": "genomescope_linear" + "tags": "genomescope_linear,Linear Plot" }, "action_type": "TagDatasetAction", "output_name": "linear_plot" }, "TagDatasetActionlog_plot": { "action_arguments": { - "tags": "genomescope_log" + "tags": "genomescope_log,Log Plot" }, "action_type": "TagDatasetAction", "output_name": "log_plot" @@ -366,28 +325,28 @@ }, "TagDatasetActionmodel_params": { "action_arguments": { - "tags": "genomescope_params" + "tags": "genomescope_params,GenomeScope Parameters" }, "action_type": "TagDatasetAction", "output_name": "model_params" }, "TagDatasetActionsummary": { "action_arguments": { - "tags": "genomescope_summ" + "tags": "genomescope_summ,GenomeScope Summary" }, "action_type": "TagDatasetAction", "output_name": "summary" }, "TagDatasetActiontransformed_linear_plot": { "action_arguments": { - "tags": "genomescope_tr_linear" + "tags": "genomescope_tr_linear,Transformed Linear Plot" }, "action_type": "TagDatasetAction", "output_name": "transformed_linear_plot" }, "TagDatasetActiontransformed_log_plot": { "action_arguments": { - "tags": "genomescope_tr_log" + "tags": "genomescope_tr_log,Transformed Log Plot" }, "action_type": "TagDatasetAction", "output_name": "transformed_log_plot" @@ -400,50 +359,49 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": \"true\", \"true_params\": \"\", \"trace_flag\": \"false\", \"num_rounds\": null}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": \"false\"}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": true, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0+galaxy1", "type": "tool", - "uuid": "460b05b9-297a-465b-aed8-6fa593cc1a3d", + "uuid": "955de351-ef19-42dc-89d7-ca213994515a", + "when": null, "workflow_outputs": [ { - "label": "GenomeScope summary", - "output_name": "summary", - "uuid": "ee35b97f-dcb1-4788-8ee1-ab8fe4391c1f" - }, - { - "label": "GenomeScope model", - "output_name": "model", - "uuid": "72ea9b21-5c3c-4d8f-8bd8-2f9cf541aadf" + "label": "GenomeScope Model Parameters", + "output_name": "model_params", + "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" }, { - "label": "GenomeScope transformed linear plot", - "output_name": "transformed_linear_plot", - "uuid": "f04a598d-3b53-4998-a2ed-825a9723d508" + "label": "GenomeScope log plot", + "output_name": "log_plot", + "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" }, { "label": "GenomeScope linear plot", "output_name": "linear_plot", - "uuid": "0c404b24-5d2b-4134-9c74-28b27e330015" + "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" }, { - "label": "GenomeScope log plot", - "output_name": "log_plot", - "uuid": "d56cb1c1-970f-486d-b662-9a47c0103b06" + "label": "GenomeScope transformed linear plot", + "output_name": "transformed_linear_plot", + "uuid": "48e2c4c5-8658-44e6-8981-673a2f1f719e" }, { "label": "GenomeScope transformed log plot", "output_name": "transformed_log_plot", - "uuid": "7f276393-5ce9-4a35-8add-9ae961269cc4" + "uuid": "ea87bd08-a6d9-4c9e-9497-8bfb1725da04" }, { - "label": "GenomeScope model parameters", - "output_name": "model_params", - "uuid": "5c681514-148e-4a9c-b392-59cc73d14b8e" + "label": "GenomeScope summary", + "output_name": "summary", + "uuid": "b74004e1-4f4b-4f43-a9f0-2a7a0a70ca1d" } ] } }, - "tags": [], - "uuid": "afd2bd57-4b6c-49f6-81aa-3a4dab50f62e", - "version": 1 -} + "tags": [ + "Reviewed", + "VGP" + ], + "uuid": "3553367b-7f97-41e7-aa93-5856b21770df", + "version": 4 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Linear_plot.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Linear_plot.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Linear_plot.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Linear_plot.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Log_plot.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Log_plot.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Log_plot.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Log_plot.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Transformed_linear_plot.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Transformed_linear_plot.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Transformed_linear_plot.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Transformed_linear_plot.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Transformed_log_plot.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Transformed_log_plot.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation/test-data/GenomeScope_Transformed_log_plot.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/test-data/GenomeScope_Transformed_log_plot.png