A Nextflow implementation of the STRling data flow:

https://github.com/quinlan-lab/STRling

STRling: a method to detect novel (and reference) STR expansions from short-read data.

Usage

To run joint calls across more than one sample on the main branch of the workflow:

nextflow run quinlan-lab/STRling-nf -r main -profile docker \
    --joint --crams 'preprocessing/*.bam' --reference GRCh38.fasta \

Alternately, -r can designate tags, e.g. -r v1.0.1.

The workflow expects the alignments to be indexed (contain a .bai/.crai) in the same directory as the .bam/.cram. It also expects the reference .fasta to be indexed (.fai) and be in the same directory as the .fasta.

Single sample, or non-joint calls, omit --joint:

nextflow run quinlan-lab/STRling-nf -r 1.0 \
    --crams 'preprocessing/*.bam' --reference GRCh38.fasta \

Complete --help docs available using:

nextflow run quinlan-lab/STRling-nf -r 1.0 --help

Output

Results of the workflow are written to <outdir>/outliers and consist of files defined in the STRling docs:

https://strling.readthedocs.io/en/latest/outputs.html