GDO Singlesample

Processing unimodal single-sample guide-derived oligonucleotide (GDO) data.

Info

ID: gdo_singlesample
Namespace: workflows/gdo

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 2.1.1 -latest \
  -main-script target/nextflow/workflows/gdo/gdo_singlesample/main.nf \
  --help

Run command

Example of params.yaml 
# Input
id: # please fill in - example: "foo"
input: # please fill in - example: "dataset.h5mu"
# layer: "foo"

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

# Filtering options
# min_counts: 200
# max_counts: 5000000
# min_guides_per_cell: 200
# max_guides_per_cell: 1500000
# min_cells_per_guide: 3

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments
nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/gdo/gdo_singlesample/main.nf \
  -params-file params.yaml
Note

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

Argument groups

Input

Name Description Attributes
--id ID of the sample. string, required, example: "foo"
--input Path to the sample. file, required, example: "dataset.h5mu"
--layer Input layer to start from. By default, .X will be used. string

Output

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

Filtering options

Name Description Attributes
--min_counts Minimum number of counts captured per cell. integer, example: 200
--max_counts Maximum number of counts captured per cell. integer, example: 5000000
--min_guides_per_cell Minimum of non-zero values per cell. integer, example: 200
--max_guides_per_cell Maximum of non-zero values per cell. integer, example: 1500000
--min_cells_per_guide Minimum of non-zero values per gene. integer, example: 3

Authors

  • Dries Schaumont (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v10(filter)
    v18(gdo_filter_with_counts)
    v25(cross)
    v35(cross)
    v41(filter)
    v71(concat)
    v49(gdo_do_filter)
    v56(cross)
    v66(cross)
    v78(cross)
    v85(cross)
    v97(cross)
    v104(cross)
    v108(Output)
    v0-->v2
    v2-->v10
    v10-->v18
    v18-->v25
    v10-->v25
    v10-->v35
    v41-->v49
    v49-->v56
    v41-->v56
    v41-->v66
    v66-->v71
    v71-->v78
    v2-->v78
    v78-->v85
    v2-->v85
    v2-->v97
    v97-->v104
    v2-->v104
    v104-->v108
    v35-->v41
    v18-->v35
    v49-->v66
    v71-->v97
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v10 fill:#e3dcea,stroke:#7a4baa;
    style v18 fill:#e3dcea,stroke:#7a4baa;
    style v25 fill:#e3dcea,stroke:#7a4baa;
    style v35 fill:#e3dcea,stroke:#7a4baa;
    style v41 fill:#e3dcea,stroke:#7a4baa;
    style v71 fill:#e3dcea,stroke:#7a4baa;
    style v49 fill:#e3dcea,stroke:#7a4baa;
    style v56 fill:#e3dcea,stroke:#7a4baa;
    style v66 fill:#e3dcea,stroke:#7a4baa;
    style v78 fill:#e3dcea,stroke:#7a4baa;
    style v85 fill:#e3dcea,stroke:#7a4baa;
    style v97 fill:#e3dcea,stroke:#7a4baa;
    style v104 fill:#e3dcea,stroke:#7a4baa;
    style v108 fill:#e3dcea,stroke:#7a4baa;