Samtools

Filter the BAM according to the instruction of scSplit via Samtools.

Info

ID: samtools
Namespace: genetic_demux

Links

Source

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 1.0.2 -latest \
  -main-script target/nextflow/genetic_demux/samtools/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
bam: # please fill in - example: "path/to/file"
# output: "$id.$key.output.output"

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

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/genetic_demux/samtools/main.nf \
  -params-file params.yaml

Note

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

Argument group

Arguments

Name	Description	Attributes
--bam	Input bam file for filtering.	file, required
--output	Samtools output directory.	file, example: "samtools_out"

Authors

• Xichen Wu (author)