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Add workflow tests for Scater QC workflow
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@pavanvidem
pavanvidem committed Dec 12, 2024
1 parent e229155 commit 0382ac8
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35 changes: 35 additions & 0 deletions topics/single-cell/tutorials/scrna-scater-qc/workflows/Single-cell-QC-with-scater-tests.yml
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- doc: Test outline for Single-cell-QC-with-scater
job:
annotation.txt:
class: File
path: test-data/annotation.txt.tabular
filetype: tabular
counts.txt:
class: File
path: test-data/counts.txt.tabular
filetype: tabular
mt_controls.txt:
class: File
path: test-data/mt_controls.txt.txt
filetype: txt
outputs:
lib_qc_plot:
asserts:
has_size:
value: 11291
delta: 500
output_loom:
asserts:
has_size:
value: 236352
delta: 10000
filtered_lib_qc_plot:
asserts:
has_size:
value: 10914
delta: 500
pca_plot:
asserts:
has_size:
value: 7106
delta: 350
344 changes: 344 additions & 0 deletions topics/single-cell/tutorials/scrna-scater-qc/workflows/Single-cell-QC-with-scater.ga
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{
"a_galaxy_workflow": "true",
"annotation": "Single-cell quality control with scater",
"comments": [],
"creator": [
{
"class": "Person",
"identifier": "0000-0002-5003-1425",
"name": "Graham Etherington"
},
{
"class": "Person",
"identifier": "0000-0003-3627-5340",
"name": "Nicola Soranzo"
},
{
"class": "Person",
"identifier": "0000-0002-5192-126X",
"name": "Pavankumar Videm"
}
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"name": "Single-cell QC with scater",
"report": {
"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
},
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "annotation.txt"
}
],
"label": "annotation.txt",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0,
"top": 39
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null}",
"tool_version": null,
"type": "data_input",
"uuid": "3575b170-465d-4e4a-bae1-ff4c1efa142a",
"when": null,
"workflow_outputs": []
},
"1": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "counts.txt"
}
],
"label": "counts.txt",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0,
"top": 159
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null}",
"tool_version": null,
"type": "data_input",
"uuid": "03bc455e-52cc-4a2e-9a00-049f0fab721f",
"when": null,
"workflow_outputs": []
},
"2": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 2,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "mt_controls.txt"
}
],
"label": "mt_controls.txt",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0,
"top": 279
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null}",
"tool_version": null,
"type": "data_input",
"uuid": "f59c9ecb-0d03-4e93-8f46-5d3ed1b75aea",
"when": null,
"workflow_outputs": []
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2",
"errors": null,
"id": 3,
"input_connections": {
"col_data": {
"id": 0,
"output_name": "output"
},
"counts": {
"id": 1,
"output_name": "output"
},
"mt_controls": {
"id": 2,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "Scater: Calculate QC metrics",
"outputs": [
{
"name": "output_loom",
"type": "loom"
}
],
"position": {
"left": 220,
"top": 39
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2",
"tool_shed_repository": {
"changeset_revision": "fd808de478b1",
"name": "scater_create_qcmetric_ready_sce",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"cell_controls\": null, \"chromInfo\": \"/tgac/services/galaxy/prod/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"col_data\": {\"__class__\": \"ConnectedValue\"}, \"counts\": {\"__class__\": \"ConnectedValue\"}, \"ercc_controls\": null, \"mt_controls\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.12.2",
"type": "tool",
"uuid": "cae20f66-087b-4c66-a317-6511b000a797",
"when": null,
"workflow_outputs": []
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
"errors": null,
"id": 4,
"input_connections": {
"input_loom": {
"id": 3,
"output_name": "output_loom"
}
},
"inputs": [],
"label": "Library QC",
"name": "Scater: plot library QC",
"outputs": [
{
"name": "output_plot",
"type": "pdf"
}
],
"position": {
"left": 550,
"top": 0
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
"tool_shed_repository": {
"changeset_revision": "2e41b35b5bdd",
"name": "scater_plot_dist_scatter",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"chromInfo\": \"/tgac/services/galaxy/prod/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_loom\": {\"__class__\": \"ConnectedValue\"}, \"plot_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.12.2",
"type": "tool",
"uuid": "60d1091e-4141-416d-9020-324f6a97abde",
"when": null,
"workflow_outputs": [
{
"label": "lib_qc_plot",
"output_name": "output_plot",
"uuid": "57113c0a-f622-42df-8a5b-5bc4329d64d4"
}
]
},
"5": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2",
"errors": null,
"id": 5,
"input_connections": {
"input_loom": {
"id": 3,
"output_name": "output_loom"
}
},
"inputs": [],
"label": "Filter SCE",
"name": "Scater: filter SCE",
"outputs": [
{
"name": "output_loom",
"type": "loom"
}
],
"position": {
"left": 665,
"top": 185
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2",
"tool_shed_repository": {
"changeset_revision": "b7ea9f09c02f",
"name": "scater_filter",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"chromInfo\": \"/tgac/services/galaxy/prod/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_type\": {\"filter_type_selector\": \"manual\", \"__current_case__\": 0, \"detection_limit\": \"4.0\", \"library_size\": \"100000\", \"expressed_genes\": \"500\", \"percent_counts_MT\": \"35.0\"}, \"input_loom\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.12.2",
"type": "tool",
"uuid": "b0cf51ed-998b-4aac-a726-5e2c93cefb34",
"when": null,
"workflow_outputs": [
{
"label": "output_loom",
"output_name": "output_loom",
"uuid": "6d503142-e29b-4c13-9773-c8176419dfb6"
}
]
},
"6": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
"errors": null,
"id": 6,
"input_connections": {
"input_loom": {
"id": 5,
"output_name": "output_loom"
}
},
"inputs": [],
"label": "Filtered Library QC",
"name": "Scater: plot library QC",
"outputs": [
{
"name": "output_plot",
"type": "pdf"
}
],
"position": {
"left": 945,
"top": 21
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
"tool_shed_repository": {
"changeset_revision": "2e41b35b5bdd",
"name": "scater_plot_dist_scatter",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"chromInfo\": \"/tgac/services/galaxy/prod/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_loom\": {\"__class__\": \"ConnectedValue\"}, \"plot_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.12.2",
"type": "tool",
"uuid": "8d3fa68e-26e0-4e1b-af9e-95bd0601b0c8",
"when": null,
"workflow_outputs": [
{
"label": "filtered_lib_qc_plot",
"output_name": "output_plot",
"uuid": "f7783f97-b108-4850-ac08-fc7d0769e8d8"
}
]
},
"7": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2",
"errors": null,
"id": 7,
"input_connections": {
"input_loom": {
"id": 5,
"output_name": "output_loom"
}
},
"inputs": [],
"label": "PCA Plot",
"name": "Scater: PCA plot",
"outputs": [
{
"name": "output_plot",
"type": "pdf"
}
],
"position": {
"left": 939,
"top": 372
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2",
"tool_shed_repository": {
"changeset_revision": "46fc6751d746",
"name": "scater_plot_pca",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"chromInfo\": \"/tgac/services/galaxy/prod/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colour_by\": \"Mutation_Status\", \"input_loom\": {\"__class__\": \"ConnectedValue\"}, \"shape_by\": \"Cell_Cycle\", \"size_by\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.12.2",
"type": "tool",
"uuid": "010f0c75-1aa5-4a53-b48c-5a7d15009ef5",
"when": null,
"workflow_outputs": [
{
"label": "pca_plot",
"output_name": "output_plot",
"uuid": "4ca6aec7-1024-4988-b975-428cfa7603ed"
}
]
}
},
"tags": [
"transcriptomics",
"single-cell"
],
"uuid": "ec8aa2ff-8e00-4f0d-896a-572a96ec0b7b",
"version": 2
}
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