Fix path resolution in check_samplesheet

[nebfield]

Before

Relative paths were resolved relative to a work directory parent

e.g. stuff/work/a1/c2/samplesheet.csv -> stuff/cineca.vcf.gz

This can be quite fragile if you change the default work directory location and is quite confusing behaviour.

It also breaks running the test profile from nextflow directly (nextflow run pgscatalog/pgsc_calc) with local files.

Now

The samplesheet path is resolved and relative genome paths are joined with the parent directory.

e.g. stuff/work/a1/c2/samplesheet.csv -> original_dir/samplesheet.csv -> original_dir/cineca.vcf.gz

New features:

• Doesn't try to resolve remote paths (s3:// or https:// prefix), trust nextflow to handle this
• Throw an error if you try to use insecure remote paths (http://)
• Will allow support for running test profile offline with nextflow run pgscatalog/pgsc_calc and nextflow run main.nf

Closes #51

[smlmbrt]

Not sure I'd really know if anything was wrong though.... better to ask Laurent? I guess the proof will be whether it works in situ

[nebfield]

yes, I think it's simplest to merge and test offline 😄