Closed nebfield closed 11 months ago
Relative paths were resolved relative to a work directory parent
e.g. stuff/work/a1/c2/samplesheet.csv -> stuff/cineca.vcf.gz
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.
nextflow run pgscatalog/pgsc_calc
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
original_dir/samplesheet.csv
original_dir/cineca.vcf.gz
New features:
s3://
https://
http://
nextflow run main.nf
Closes #51
yes, I think it's simplest to merge and test offline 😄
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:
s3://
orhttps://
prefix), trust nextflow to handle thishttp://
)nextflow run pgscatalog/pgsc_calc
andnextflow run main.nf
Closes #51