...
Use threads and redirect STDOUT to a file (line 6)
Clair3
Clair3 is available in a nextflow pipeline:
epi2me-labs/wf-human-snp: Small variant calling for human samples (github.com)
The pipeline’s configuration is to run in the local process and not submit jobs - will need to test if the overhead of PBS compares with running “locally” in a job.
Using test data:
| Code Block |
|---|
nextflow run epi2me-labs/wf-human-snp -profile singularity \
--bam /work/ont/clair3/sample_data/chr6_chr20.bam \
--bed /work/ont/clair3/sample_data/chr6_chr20.bed \
--ref /work/ont/clair3/sample_data/chr6_chr20.fasta \
--out_dir "results" \
--process.executor "pbspro" |
Line 1: Use singularity for the pipeline software
Line 5: save results in the results folder
Line 6: use PBS to run the processes