Rna multisample

Processing unimodal multi-sample RNA transcriptomics data.

Info

ID: rna_multisample
Namespace: multiomics

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -main-script ./workflows/multiomics/rna_multisample/main.nf \
  --help

Run command

Example of params.yaml
# Inputs
id: # please fill in - example: "concatenated"
input: # please fill in - example: "dataset.h5mu"

# Output
# output: "$id.$key.output.h5mu"

# Filtering highly variable genes
filter_with_hvg_var_output: "filter_with_hvg"
filter_with_hvg_obs_batch_key: "sample_id"
filter_with_hvg_flavor: "seurat"
# filter_with_hvg_n_top_genes: 123

# QC metrics calculation options
var_qc_metrics: ["filter_with_hvg"]
top_n_vars: [50, 100, 200, 500]

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script ./workflows/multiomics/rna_multisample/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name Description Attributes
--id ID of the concatenated file string, required, example: "concatenated"
--input Path to the samples. file, required, example: "dataset.h5mu"

Output

Name Description Attributes
--output Destination path to the output. file, required, example: "output.h5mu"

Filtering highly variable genes

Name Description Attributes
--filter_with_hvg_var_output In which .var slot to store a boolean array corresponding to the highly variable genes. string, default: "filter_with_hvg"
--filter_with_hvg_obs_batch_key If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = ‘seurat_v3’, ties are broken by the median (across batches) rank based on within-batch normalized variance. string, default: "sample_id"
--filter_with_hvg_flavor 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. string, default: "seurat"
--filter_with_hvg_n_top_genes Number of highly-variable genes to keep. Mandatory if filter_with_hvg_flavor is set to ‘seurat_v3’. integer

QC metrics calculation options

Name Description Attributes
--var_qc_metrics Keys to select a boolean (containing only True or False) column from .var. For each cell, calculate the proportion of total values for genes which are labeled ‘True’, compared to the total sum of the values for all genes. List of string, default: "filter_with_hvg", example: "ercc,highly_variable", multiple_sep: ","
--top_n_vars Number of top vars to be used to calculate cumulative proportions. If not specified, proportions are not calculated. --top_n_vars 20,50 finds cumulative proportion to the 20th and 50th most expressed vars. List of integer, default: 50, 100, 200, 500, multiple_sep: ","

Authors

  • Dries De Maeyer (author)

  • Robrecht Cannoodt (author, maintainer)

  • Dries Schaumont (author)

Visualisation

flowchart LR
    v0(Input)
    v3(toSortedList)
    v5(flatMap)
    v7(toSortedList)
    v9(Output)
    v15(normalize_total)
    v17(join)
    v26(log1p)
    v28(join)
    v37(delete_layer)
    v39(join)
    v48(filter_with_hvg)
    v50(join)
    v59(rna_calculate_qc_metrics)
    v61(join)
    v68(Output)
    v0-->v3
    v3-->v5
    v5-->v7
    v7-->v9
    v5-->v17
    v5-->v15
    v15-->v17
    v17-->v28
    v17-->v26
    v26-->v28
    v28-->v39
    v28-->v37
    v37-->v39
    v39-->v50
    v39-->v48
    v48-->v50
    v50-->v61
    v50-->v59
    v59-->v61
    v61-->v68