Output files

The workflow will create the following in the directory you launch the pipeline from.

results/         # main output (default --outdir)
logs/            # LSF stdout and stderr, and the Nextflow log

Intermediate output is written to the working directory, on HPC /re_scratch/$USER (default -work-dir)

For each query gene and build, the main output is an annotated list of variants, and a multi-sample VCF file and index.

GENOMEBUILD_HGNCSYMBOL_ENSEMBLID_annotated_variants.tsv
GENOMEBUILD_HGNCSYMBOL_ENSEMBLID_left_norm_tagged.vcf.gz
GENOMEBUILD_HGNCSYMBOL_ENSEMBLID_left_norm_tagged.vcf.gz.tbi

When --publish_all true, the output of every process is written to a folder with process name, within results/ (default --outdir).