A Nextflow implementation of the STRling data flow:
https://github.com/quinlan-lab/STRling
STRling: a method to detect novel (and reference) STR expandsions from short-read data.
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
Results of the workflow are written to <outdir>/outliers and
consist of files defined in the STRling docs: