diff --git a/topics/single-cell/tutorials/scrna-scater-qc/data-library.yaml b/topics/single-cell/tutorials/scrna-scater-qc/data-library.yaml index 012f128879a5e7..4b80956374c0e5 100644 --- a/topics/single-cell/tutorials/scrna-scater-qc/data-library.yaml +++ b/topics/single-cell/tutorials/scrna-scater-qc/data-library.yaml @@ -15,15 +15,15 @@ items: - name: 'DOI: 10.5281/zenodo.3386291' description: latest items: - - url: https://zenodo.org/api/files/83bb489c-cd94-4d33-b8f4-da1dd7ee8e2b/annotation.txt + - url: https://zenodo.org/records/3386291/files/annotation.txt src: url ext: txt info: https://doi.org/10.5281/zenodo.3386291 - - url: https://zenodo.org/api/files/83bb489c-cd94-4d33-b8f4-da1dd7ee8e2b/counts.txt + - url: https://zenodo.org/records/3386291/files/counts.txt src: url ext: txt info: https://doi.org/10.5281/zenodo.3386291 - - url: https://zenodo.org/api/files/83bb489c-cd94-4d33-b8f4-da1dd7ee8e2b/mt_controls.txt + - url: https://zenodo.org/records/3386291/files/mt_controls.txt src: url ext: txt info: https://doi.org/10.5281/zenodo.3386291 diff --git a/topics/single-cell/tutorials/scrna-scater-qc/tutorial.md b/topics/single-cell/tutorials/scrna-scater-qc/tutorial.md index f99efaa5e08b1c..e0422cc1da05b3 100644 --- a/topics/single-cell/tutorials/scrna-scater-qc/tutorial.md +++ b/topics/single-cell/tutorials/scrna-scater-qc/tutorial.md @@ -7,6 +7,10 @@ priority: 1 redirect_from: - /topics/transcriptomics/tutorials/scrna-scater-qc/tutorial zenodo_link: 'https://zenodo.org/record/3386291' +answer_histories: + - label: "UseGalaxy.eu" + history: https://singlecell.usegalaxy.eu/u/videmp/h/single-cell-qc-with-scater + date: 2024-12-12 tags: questions: - How to ensure the quality of single-cell RNA-seq data? @@ -32,12 +36,13 @@ time_estimation: 1H key_points: - Single-cell RNA-seq data is often noisy - scater can be used to apply the visualise-filter-visualise paradigm of quality control -contributors: -- ethering -- nsoranzo - +contributions: + authorship: + - ethering + - nsoranzo + testing: + - pavanvidem gitter: Galaxy-Training-Network/galaxy-single-cell - --- diff --git a/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow-tests.yml b/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow-tests.yml new file mode 100644 index 00000000000000..1a25e0af54f02c --- /dev/null +++ b/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow-tests.yml @@ -0,0 +1,35 @@ +- doc: Test outline for Single-cell-QC-with-scater + job: + annotation.txt: + class: File + location: https://zenodo.org/records/3386291/files/annotation.txt + filetype: tabular + counts.txt: + class: File + location: https://zenodo.org/records/3386291/files/counts.txt + filetype: tabular + mt_controls.txt: + class: File + location: https://zenodo.org/records/3386291/files/mt_controls.txt + filetype: txt + outputs: + lib_qc_plot: + asserts: + has_size: + value: 11291 + delta: 500 + output_loom: + asserts: + has_size: + value: 236352 + delta: 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