cgmlst-clustering

cgmlst-clustering takes the combined allele profile from the output of the kma-cgmlst pipeline, calculate distance and perform dendrogram and clustering.

The distance is calculated by cgmlst-dists.

You can specify pairwise comparison to count missing as differences by using mode parameter.

Input

Arguments	Usage
cgmlst	a combined allele profile calls from the kma-cgmlst pipeline, in .csv format
threshold	threshold for AgglomerativeClustering, can be a list of numbers in a quotation, e.g. '5 10 15'
outdir	output directory
runClustering	a single argument that specify if clustering should be run
linkage_type	linkage type for AgglomerativeClustering, possible choice is 'single', 'average', 'complete'
mode	if mode="count-missing" then pairwise comparison includes missing, otherwise it ignores missing

Usage

For initial run without clustering:

nextflow run BCCDC-PHL/cgmlst-clustering --cgmlst <path/to/combined_cgmlst.csv> --outdir <path/to/output_dir>

This will produce a dendrogram for examining.

For rerunning with clustering after determining the thresholds from looking at the dendrogram, add all arguments for clusterings and -resume to continue the nextflow pipeline from cache:

nextflow run BCCDC-PHL/cgmlst-clustering \
  --cgmlst <path/to/combined_cgmlst.csv> \
  --runClustering \
  --threshold '25 50 75 100 125 150 200 250 300 350 400' \
  --linkage_type 'single' \
  --outdir <path/to/output_dir> \ 
  -resume

Sample sheet

You can supply a samplesheet.csv to specify which samples are to be included for clustering. Samplesheet.csv can follow the same format as those for [kma-cgmlst] (https://github.com/BCCDC-PHL/kma-cgmlst), i.e, three columns with ID,R1,R2. Or it could a csv with only one column ID. When running the pipeline using samplesheet input, use --samplesheet_input flag:

nextflow run BCCDC-PHL/cgmlst-clustering \
  --cgmlst <path/to/combined_cgmlst.csv> \
  --outdir <path/to/output_dir> \
  --samplesheet_input <path/to/samplesheet.csv>

or

nextflow run BCCDC-PHL/cgmlst-clustering \
  --cgmlst <path/to/combined_cgmlst.csv> \
  --runClustering \
  --threshold '25 50 75 100 125 150 200 250 300 350 400' \
  --linkage_type 'single' \
  --outdir <path/to/output_dir> \ 
  --samplesheet_input <path/to/samplesheet.csv> \
  -resume