Output¶

After VIP completes successfully the path specified by --output contains content similar to:

.nextflow
.nxf.home
.nxf.log
.nxf.tmp
.nxf.work
intermediates
nxf_report.html
nxf_timeline.html
my_project_id.html
my_project_id.vcf.gz
my_project_id.vcf.gz.csi

Report¶

For each project defined in your --input sample-sheet a set of three files is created:

my_project.html
my_project.vcf.gz
my_project.vcf.gz.csi

In case no project identifiers were supplied these files will be called:

vip.html
vip.vcf.gz
vip.vcf.gz.csi

vip.html is an interactive report based on vip.vcf.gz that can be viewed in any modern browser
vip.vcf.gz contains annotated candidate variants for interpretation
vip.vcf.gz.csi is the corresponding index file

By default, the report is a self-contained .html file that does not depend on external websites. All data and code to interact with and display this data is contained in one file. This ensures that no internet connection is required to view the report and enables easy sharing with other people.

Example report

Above: report example

Intermediates¶

VIP publishes selected intermediate results to allow reanalysis using the vcf.start parameter. Additionaly these results can be used to understand why variant records did not make it into the report.

The content of the intermediates directory depends on the used --workflow and looks similar to:

hlhs_famA_grch38_annotations.vcf.gz
hlhs_famA_grch38_annotations.vcf.gz.csi
hlhs_famA_grch38_classifications.vcf.gz
hlhs_famA_grch38_classifications.vcf.gz.csi
hlhs_famA_grch38_famA_sample0_small_variants.vcf.gz
hlhs_famA_grch38_famA_sample0_small_variants.vcf.gz.csi
hlhs_famA_grch38_famA_sample0_sv.vcf.gz
hlhs_famA_grch38_famA_sample0_sv.vcf.gz.csi
hlhs_famA_grch38_famA_sample1_small_variants.vcf.gz
hlhs_famA_grch38_famA_sample1_small_variants.vcf.gz.csi
hlhs_famA_grch38_famA_sample1_sv.vcf.gz
hlhs_famA_grch38_famA_sample1_sv.vcf.gz.csi
hlhs_famA_grch38_famA_sample2_small_variants.vcf.gz
hlhs_famA_grch38_famA_sample2_small_variants.vcf.gz.csi
hlhs_famA_grch38_famA_sample2_sv.vcf.gz
hlhs_famA_grch38_famA_sample2_sv.vcf.gz.csi

Other¶

Besides the result files and intermediate files the following data is generated:

.nextflow
.nxf.home
.nxf.log
.nxf.tmp
.nxf.work
nxf_report.html
nxf_timeline.html

For details, see the Nextflow documentation.