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hubmapconsortium / azimuth-annotate

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How to use " cwltool pipeline.cwl" with in-house human PBMC CITE-Seq data ? #1

Closed qicheng-ma closed 2 years ago

qicheng-ma commented 2 years ago

Dear Austin,

I have both cwltool and azimuth-annotate installed:

cwltool pipeline.cwl INFO /mnt/efs/home/stb3865/software/anaconda3/bin/cwltool 3.1.20211107152837 INFO Resolved 'pipeline.cwl' to 'file:///mnt/efs/home/stb3865/software/azimuth-annotate/pipeline.cwl' usage: pipeline.cwl [-h] --matrix MATRIX --reference REFERENCE --secondary-analysis-matrix SECONDARY_ANALYSIS_MATRIX [job_order] pipeline.cwl: error: the following arguments are required: --matrix, --reference, --secondary-analysis-matrix

I have the in-house human PBMC CITE-Seq data, here are my questions:

1) For human PBMC (https://seurat.nygenome.org/azimuth/references/v1.0.0/human_pbmc), what would the two-level code be ? 2) Am I right if I supply scRNA matrix for --matrix and ADT matrix for --secondary-analysis-matrix ?

Thanks in advance!

AustinHartman commented 2 years ago

Hi, azimuth-annotate is used to annotate datasets which come from a specific HuBMAP pipeline and so if you have processed your data in some other way azimuth-annotate will not work. I would recommend you try uploading your dataset to the azimuth web app here: https://app.azimuth.hubmapconsortium.org/app/human-pbmc. If you are curious what code the azimuth web app used to process your data, you can download that after running under "Download Results" -> "Analysis script template"