diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/.dockstore.yml b/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/.dockstore.yml deleted file mode 100644 index 2ce077b68..000000000 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/.dockstore.yml +++ /dev/null @@ -1,8 +0,0 @@ -version: 1.2 -workflows: -- name: main - primaryDescriptorPath: /meryldb-creation-trio.ga - subclass: Galaxy - testParameterFiles: - - /meryldb-creation-trio-tests.yml - publish: true diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/meryldb-creation-trio-tests.yml b/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/meryldb-creation-trio-tests.yml deleted file mode 100644 index 05fafc37f..000000000 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/meryldb-creation-trio-tests.yml +++ /dev/null @@ -1,132 +0,0 @@ -- doc: Test outline for meryl_database_creation_trios.ga - job: - Collection of Paired Reads - Maternal: - class: Collection - collection_type: 'list:paired' - elements: - - class: Collection - type: paired - identifier: paired_maternal - elements: - - identifier: forward - class: File - location: https://zenodo.org/record/6603774/files/paternal.fastq?download=1 - filetype: fastqsanger - - identifier: reverse - class: File - location: https://zenodo.org/record/6603774/files/paternal.fastq?download=1 - filetype: fastqsanger - Collection of Paired Reads - Paternal: - class: Collection - collection_type: 'list:paired' - elements: - - class: Collection - type: paired - identifier: paired_paternal - elements: - - identifier: forward - class: File - location: https://zenodo.org/record/6603774/files/maternal.fastq?download=1 - filetype: fastqsanger - - identifier: reverse - class: File - location: https://zenodo.org/record/6603774/files/maternal.fastq?download=1 - filetype: fastqsanger - Pacbio Hifi reads: - class: Collection - collection_type: list - elements: - - class: File - identifier: pacbio_dataset - location: https://zenodo.org/record/6603774/files/child.fastq?download=1 - filetype: fastqsanger - 'K-mer length ': 9 - Ploidy: 1 - outputs: - GenomeScope linear plot (maternal): - class: File - file: test-data/GenomeScope_Linear_plot_maternal.png - compare: sim_size - delta: 15000 - GenomeScope log plot (maternal): - class: File - file: test-data/GenomeScope_Log_plot_maternal.png - compare: sim_size - delta: 15000 - GenomeScope transformed linear plot (maternal): - class: File - file: test-data/GenomeScope_Transformed_linear_plot_maternal.png - compare: sim_size - delta: 15000 - GenomeScope transformed log plot (paternal): - class: File - file: test-data/GenomeScope_Transformed_linear_plot_paternal.png - compare: sim_size - delta: 15000 - GenomeScope linear plot (paternal): - class: File - file: test-data/GenomeScope_Linear_plot_paternal.png - compare: sim_size - delta: 15000 - GenomeScope log plot (paternal): - class: File - file: test-data/GenomeScope_Log_plot_paternal.png - compare: sim_size - delta: 15000 - GenomeScope transformed linear plot (paternal): - class: File - file: test-data/GenomeScope_Transformed_linear_plot_paternal.png - compare: sim_size - delta: 15000 - GenomeScope transformed log plot (paternal): - class: File - file: test-data/GenomeScope_Transformed_linear_plot_paternal.png - compare: sim_size - delta: 15000 - GenomeScope linear plot (child): - class: File - file: test-data/GenomeScope_Linear_plot_child.png - compare: sim_size - delta: 15000 - GenomeScope log plot (child): - class: File - file: test-data/GenomeScope_Log_plot_child.png - compare: sim_size - delta: 15000 - GenomeScope transformed linear plot (child): - class: File - file: test-data/GenomeScope_Transformed_linear_plot_child.png - compare: sim_size - delta: 15000 - GenomeScope transformed log plot (child): - class: File - file: test-data/GenomeScope_Transformed_linear_plot_child.png - compare: sim_size - delta: 15000 - GenomeScope summary (child): - asserts: - has_text: - text: '39,419 bp' - has_text: - text: '43,763 bp' - GenomeScope model (child): - asserts: - has_text: - text: '1.212e+01' - has_text: - text: '3.165e-01' - Meryl read-db.meryldb: - asserts: - has_size: - value: 205051 - delta: 1000 - Meryl pat.meryldb: - asserts: - has_size: - value: 40338 - delta: 1000 - Meryl mat.meryldb: - asserts: - has_size: - value: 49534 - delta: 1000 diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/.dockstore.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/.dockstore.yml new file mode 100644 index 000000000..9e540d8cc --- /dev/null +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/.dockstore.yml @@ -0,0 +1,7 @@ +version: 1.2 +workflows: +- name: main + primaryDescriptorPath: /kmer-profiling-hifi-trio-VGP2.ga + subclass: Galaxy + testParameterFiles: + - /kmer-profiling-hifi-trio-VGP2-tests.yml diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/.workflowhub.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/.workflowhub.yml similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/.workflowhub.yml rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/.workflowhub.yml diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md similarity index 57% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/CHANGELOG.md rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md index aa79d8016..77584b36a 100644 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md @@ -6,6 +6,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## [0.1] - 2023-10-30 + +### Added +- Clearer labels + +### Removed +- Interlacing step that was unneccessary +- Requirement for paired list inputs for the Illumina parental reads. A dataset collection list is sufficient now. +- Unnecessary workflow intputs ## [0.1] - 2021-08-26 ### Added diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/README.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/README.md similarity index 79% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/README.md rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/README.md index c49519361..3893ef5f5 100644 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/README.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/README.md @@ -4,9 +4,9 @@ This workflow collects the metrics on the properties of the genome under conside ### Inputs -- Collection of Hifi long reads in FASTQ format -- Paternal short-read Illumina sequencing reads in FASTQ format -- Maternal short-read Illumina sequencing reads in FASTQ format +- Collection of Hifi long reads [fastq] (Collection) +- Paternal short-read Illumina sequencing reads [fastq] (Collection) +- Maternal short-read Illumina sequencing reads [fastq] (Collection) ### Outputs diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml new file mode 100644 index 000000000..1d9044cfb --- /dev/null +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml @@ -0,0 +1,73 @@ +- doc: Test outline for kmer-profiling-hifi-trio-VGP2.ga + job: + Maternal reads: + class: Collection + collection_type: list + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/6603774/files/paternal.fastq?download=1 + filetype: fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/record/6603774/files/paternal.fastq?download=1 + filetype: fastqsanger + Paternal reads: + class: Collection + collection_type: list + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/6603774/files/maternal.fastq?download=1 + filetype: fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/record/6603774/files/maternal.fastq?download=1 + filetype: fastqsanger + Pacbio Hifi reads: + class: Collection + collection_type: list + elements: + - class: File + identifier: pacbio_dataset + location: https://zenodo.org/record/6603774/files/child.fastq?download=1 + filetype: fastqsanger + 'K-mer length': 9 + Ploidy: 1 + outputs: + GenomeScope linear plot (maternal): + class: File + file: test-data/GenomeScope_Linear_plot_maternal.png + compare: sim_size + delta: 15000 + GenomeScope linear plot (paternal): + class: File + file: test-data/GenomeScope_Linear_plot_paternal.png + compare: sim_size + delta: 15000 + GenomeScope linear plot (child): + class: File + file: test-data/GenomeScope_Linear_plot_child.png + compare: sim_size + delta: 15000 + GenomeScope summary (child): + asserts: + has_text: + text: '39,419 bp' + has_text: + text: '43,763 bp' + 'Meryl database : Child': + asserts: + has_size: + value: 205051 + delta: 1000 + 'Meryl database : paternal': + asserts: + has_size: + value: 40338 + delta: 1000 + 'Meryl database : maternal': + asserts: + has_size: + value: 49534 + delta: 1000 diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/meryldb-creation-trio.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga similarity index 66% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/meryldb-creation-trio.ga rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga index 91c7db771..f919c1377 100644 --- a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/meryldb-creation-trio.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga @@ -12,148 +12,128 @@ "name": "Galaxy" } ], - "release": "0.1", "format-version": "0.1", "license": "CC-BY-4.0", - "name": "Quality Evaluation For Trio Assembly", + "release": "0.1.1", + "name": "kmer-profiling-hifi-trio-VGP2", "steps": { "0": { - "annotation": "K-mer length used to calculate k-mer spectra. 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log plot (child)", "output_name": "log_plot", - "uuid": "543a3133-55d8-404d-a55b-73ecc7082c06" + "uuid": "4fc5e47d-bae4-44f3-957b-4dce5068610a" + }, + { + "label": "GenomeScope Model Parameters (child)", + "output_name": "model_params", + "uuid": "3bc4131f-ce9b-4358-a20b-885020d34f09" } ] }, - "12": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, - "id": 12, + "id": 10, "input_connections": { "operation_type|input_meryldb_02": { - "id": 9, + "id": 7, "output_name": "read_db" } }, @@ -811,14 +613,8 @@ } ], "position": { - "bottom": 1097.0625, - "height": 113.5625, - "left": 614.5, - "right": 814.5, - "top": 983.5, - "width": 200, - "x": 614.5, - "y": 983.5 + "left": 1303.27734375, + "top": 1097.121924999974 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -837,17 +633,18 @@ "tool_state": "{\"operation_type\": {\"command_type\": \"groups-kmers\", \"__current_case__\": 3, \"groups_operations\": \"union-sum\", 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@@ -1110,12 +887,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool GenomeScope", - "name": "input" - } - ], + "inputs": [], "label": "Genomescope on maternal haplotype", "name": "GenomeScope", "outputs": [ @@ -1145,14 +917,8 @@ } ], "position": { - "bottom": 1624.0625, - "height": 550.59375, - "left": 1153.484375, - "right": 1353.484375, - "top": 1073.46875, - "width": 200, - "x": 1153.484375, - "y": 1073.46875 + "left": 1841.77734375, + "top": 1187.106299999974 }, "post_job_actions": { "HideDatasetActionmodel": { @@ -1215,35 +981,39 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": \"false\", \"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\": false, \"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": "8ae9060f-ec62-4968-998e-50f44f2b3ab9", + "uuid": "87497ba1-5c23-4852-9e2f-0bd78dc86753", + "when": null, "workflow_outputs": [ + { + "label": "GenomeScope log plot (maternal)", + "output_name": "log_plot", + "uuid": "e2ef48ab-bbb8-4a89-8d10-4de7998db481" + }, { "label": "GenomeScope transformed log plot (maternal)", "output_name": "transformed_log_plot", - "uuid": "ca60f7ce-a7e2-4368-8b03-62b32156d771" + "uuid": "ebe91290-a02b-498d-adb6-75fab0739fbf" }, { "label": "GenomeScope transformed linear plot (maternal)", "output_name": "transformed_linear_plot", - "uuid": "b52b3f93-8aaa-49dd-b420-d14001b8458d" + "uuid": "7ecb789d-57e3-40f2-81ff-f853b444609b" }, { "label": "GenomeScope linear plot (maternal)", "output_name": "linear_plot", - "uuid": "1e6c2417-b969-4c11-81c3-be9ef11c650c" - }, - { - "label": "GenomeScope log plot (maternal)", - "output_name": "log_plot", - "uuid": "4d8cff3d-d968-467c-94a0-95f3110f2ac5" + "uuid": "ed208558-8a6f-4405-bd9c-7e6343e9f71d" } ] } }, - "tags": [], - "uuid": "8da74177-a675-42a2-a187-2514ea64d6bd", - "version": 4 -} + "tags": [ + "Reviewed", + "VGP" + ], + "uuid": "af01815b-5b66-4578-ade7-6e2caed0c19a", + "version": 9 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Linear_plot_child.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Linear_plot_child.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Linear_plot_child.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Linear_plot_child.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Linear_plot_maternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Linear_plot_maternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Linear_plot_maternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Linear_plot_maternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Linear_plot_paternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Linear_plot_paternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Linear_plot_paternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Linear_plot_paternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Log_plot_child.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Log_plot_child.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Log_plot_child.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Log_plot_child.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Log_plot_maternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Log_plot_maternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Log_plot_maternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Log_plot_maternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Log_plot_paternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Log_plot_paternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Log_plot_paternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Log_plot_paternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_linear_plot_child.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_linear_plot_child.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_linear_plot_child.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_linear_plot_child.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_linear_plot_maternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_linear_plot_maternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_linear_plot_maternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_linear_plot_maternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_linear_plot_paternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_linear_plot_paternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_linear_plot_paternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_linear_plot_paternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_log_plot_child.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_log_plot_child.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_log_plot_child.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_log_plot_child.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_log_plot_maternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_log_plot_maternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_log_plot_maternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_log_plot_maternal.png diff --git a/workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_log_plot_paternal.png b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_log_plot_paternal.png similarity index 100% rename from workflows/VGP-assembly-v2/VGP-meryldb-creation-trio/test-data/GenomeScope_Transformed_log_plot_paternal.png rename to workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/test-data/GenomeScope_Transformed_log_plot_paternal.png