Codeplot
Introduction
Script
Input
Output
hvg
Introduction

this workflow accepts h5fd file and annotate highly variable genes ,regress out (mostly) unwanted sources of variation then cale data to unit variance and zero mean with sc.pp.highly_variable_genes ,sc.pp.regress_out and sc.pp.scale.

Script
Input
Task nameAttribute nameTypeDescription
*
      main
    project_nameString
      project name
    
*
      main
    anndataFile
      Input object format：anndata
    
*
      main.hvg
    subsetBoolean
      Inplace subset to highly-variable genes if True otherwise merely indicate highly variable genes.
    
*
      main.hvg
    n_top_genesInt
      Number of highly-variable genes to keep. Mandatory if flavor='seurat_v3'.
    
*
      main.hvg
    min_meanFloat
      If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.
    
*
      main.hvg
    min_dispFloat
      If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.
    
*
      main.hvg
    memoryString
      Number of memory running tasksnotice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8
    
*
      main.hvg
    max_valueFloat
      Clip (truncate) to this value after scaling. If None, do not clip.
    
*
      main.hvg
    max_meanFloat
      If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.
    
*
      main.hvg
    max_dispFloat
      If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.
    
*
      main.hvg
    flavorString
      ['seurat', 'cell_ranger', 'seurat_v3'],Choose the flavor for identifying highly variable genes. For the dispersion based methods in their default workflows, Seurat passes the cutoffs whereas Cell Ranger passes n_top_genes.
    
*
      main.hvg
    dockerString
      --
    
*
      main.hvg
    cpuString
      Number of CPU running tasks.notice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8
    
Output
Task nameAttribute nameTypeDescription
*
      main
    pngfileArray[File]
      Return the output file to the column name of the corresponding table by this.xxx
    
*
      main
    h5adfileFile
      Return the output file to the column name of the corresponding table by this.xxx