Error when running on WGS

[alohasiqi]

Description of the bug

Hi!

I have been trying to run the workflow on my WGS samples using singularity on HPC but it keeps throwing out errors.

Can you help direct me with the right to run the workflow on WGS? I would greatly appreciate your help.

1. I have tested on my vcf file, but it gives some error

ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (sle chromosome)'
Error: Missing --chr argument.

the code is
nextflow run pgscatalog/pgsc_calc \ -profile singularity \ -latest \ --input code/samplesheet.csv --target_build GRCh38 \ --pgs_id PGS000328 \ --parallel -c code/my_custom.config

the sampleshee.csv is
sampleset,path_prefix,chrom,format
sle,mypath/sle, ,vcf

2. when converting the vcf to bfiles, it gives another error
   ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE (sle)'

the sampleshee.csv is
sampleset,path_prefix,chrom,format
sle,mypath/sle,22,bfile

Command used and terminal output

No response

Relevant files

No response

System information

No response

[nebfield]

Your first samplesheet contains a space in the chromosome field:

sle,mypath/sle, ,vcf

So the workflow is trying to extract variants from chromosome " " (which doesn't exist). Delete the space and it should be OK.

However, WGS data are not yet well supported by the calculator, which is probably why you get an error on the MATCH_COMBINE step. If you'd like to use the calculator with WGS data it's best to preprocess your VCF to include non-variant sites (the docs have a link describing how to do this).

[ashenfernando1]

@nebfield Just wanted to clarify whether supporting WGS natively on pgsc_calc is still on the roadmap, because there's a not planned tag on this thread, thank you.

[nebfield]

Yes, native support for WGS is on the roadmap for the new year 😄

[smlmbrt]

Created a placeholder issue: #396