Multiple custom scorefiles on the cloud

[geocarvalho]

Hi, I am running pgsc_calc on AWS HealthOmics and I am not sure how to set up the multiple custom scorfiles. What is the recommendation to run multiple scorefiles without using glob? For example using the bash:

nextflow run main.nf --format json --input /home/ssm-user/gvcn/pgsc_calc/parameter-input.json --hg38_chain /home/ssm-user/gvcn/hg38ToHg19.over.chain.gz --scorefile /home/ssm-user/gvcn/PGS000004.txt --scorefile /home/ssm-user/gvcn/PGS003725.txt --target_build GRCh38 --run_ancestry /home/ssm-user/gvcn/pgsc_HGDP+1kGP_v1.tar.zst -profile docker

Thanks!

[nebfield]

The only supported method of working with multiple custom scoring files is by using quoted wildcards:

--scorefile "/home/ssm-user/gvcn/PGS*.txt"

Nextflow handles the globs to set up the file paths.

[geocarvalho]

There is any recomendation on how to combine custom scores so I can set just one file? --scorefile /home/ssm-user/gvcn/PGS_combined.txt

Thanks!

[nebfield]

Not currently! It's important that each scoring file is separate. The calculator combines them internally for parallel calculation.

If putting the custom files in a single directory is a problem perhaps creating symlinks might be a useful workaround.