v-pagano/happy-compare

Happy-Compare Documentation

Initial setup

The repository is on github. Simply clone that repo and you can run the pipeline.

git clone [email protected]:v-pagano/happy-compare.git

Running a simple pipeline

Everything is setup in the input csv file, with that running the pipeline is simple. Just identify the input file and where you would like the output files to be written

nextflow run main.nf --input samples.csv --outputFolder /scratch/myFolder/output

CSV Format

The input csv file is setup with one row per sample. Many columns have a default if the field is left blank sampleId,truthVcf,bedFile,chromosome,stratifications,reference,SDF,GATK,DV,SBPAN,SBAI,HPRCDV,HPRCDTrio

Column	Description	Default
sampleId	Sample identifier
truthVcf	True variants for comparison
bedFile	.bed file for comparison locations	HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
chromosome	chromosomes to compare	All chromosomes
stratifications	tsv of bed files for stratification	v3.1-GRCh38-stratifications-all-except-genome-specific-stratifications.tsv
reference	genome reference .fa file	GRCh38tgen_decoy_alts_hla.fa
SDF	SDF folder for comparison	GRCh38tgen_decoy_alts_hla.sdf

The rest of the columns are the comparisons that you want to do with the column name as the tag for that sample and the field with the vcf file to test. Take a look at HG002-happy.csv for an example.

Output files

The output files will all end up in the outputFolder that you specified. They will be named sampleId-comparisonTag-chromosome.*

Profiles

Profiles allow you to tailor how to run the pipeline. Simply add -profile profileName to your command line to use them, for example:

nextflow run main.nf --input samples.csv --outputFolder /scratch/myFolder/output -profile gemini 

Here are the current profiles you can use:

Profile	Modifications
dback	Configured for the dback cluster
gemini	Configured for the gemini cluster
reports	Outputs reports on CPU usage and elapsed time