Start running¶
After installation, it is time for a quick test to verify that VIP works using some test data.
Input¶
To run VIP you need to provide at least workflow, input and output arguments (described in detail here). The following example processes a collection of .vcf files.
cd vip
vip --workflow vcf --input test/resources/multiproject.tsv --output output_multiproject
Output¶
Executing the above command displays progress until the pipeline completes.
N E X T F L O W ~ version 22.10.6
Launching `vip_vcf.nf` [disturbed_khorana] DSL2 - revision: 8f8c80809c
executor > local (27)
[- ] process > samtools_index -
[71/4bb8b5] process > vcf:convert (2) [100%] 5 of 5 ✔
[c7/1f8dc7] process > vcf:index (1) [100%] 1 of 1 ✔
[ad/51639f] process > vcf:stats (1) [100%] 2 of 2 ✔
[54/a6c17d] process > vcf:merge_vcf (1) [100%] 1 of 1 ✔
[a5/790ba1] process > vcf:merge_gvcf (1) [100%] 1 of 1 ✔
[- ] process > vcf:split -
[64/dafd8f] process > vcf:normalize (2) [100%] 2 of 2 ✔
[c4/ed6e06] process > vcf:annotate (1) [100%] 2 of 2 ✔
[43/c63075] process > vcf:classify (2) [100%] 2 of 2 ✔
[66/3adcef] process > vcf:filter (2) [100%] 2 of 2 ✔
[d1/1d89ee] process > vcf:inheritance (1) [100%] 2 of 2 ✔
[d7/d717a0] process > vcf:classify_samples (1) [100%] 2 of 2 ✔
[45/0564f9] process > vcf:filter_samples (1) [100%] 2 of 2 ✔
[- ] process > vcf:concat -
[- ] process > vcf:slice -
[ad/fc2b6c] process > vcf:report (2) [100%] 3 of 3 ✔
Duration : 1m 00s
CPU hours : 0.2
Succeeded : 27
Results¶
ls -1 output_multiproject/
The output folder contains one report for each project described in test/resources/multiproject.tsv.
intermediates
nxf_report.html
nxf_timeline.html
vip0.html
vip0.vcf.gz
vip0.vcf.gz.csi
vip1.html
vip1.vcf.gz
vip1.vcf.gz.csi
vip2.html
vip2.vcf.gz
vip2.vcf.gz.csi
The files vip0.html, vip1.html and vip2.html can be opened in your browser and display an interactive report based on the corresponding .vcf.gz output files.
The outputs are described in more detail here.