search

dnanexus / dxCompiler

WDL and CWL compiler for the DNAnexus platform
Apache License 2.0
31 stars 17 forks source link

UK Biobank RAP path with spaces in it #454

Closed nshrine closed 1 year ago

nshrine commented 1 year ago

How do I get dxCompiler to accept a path with spaces in it? e.g.

Array[File]+ bgens = ["dx://project-GJbvyPjJy3Gy01jz4x8bXzgv:/Bulk/Imputation/UKB imputation from genotype/ukb22828_c10_b0_v3.bgen","dx://project-GJbvyPjJy3Gy01jz4x8bXzgv:/Bulk/Imputation/UKB imputation from genotype/ukb22828_c6_b0_v3.bgen",

Below doesn't work nor does one \ or 4 \\

Array[File]+ bgens = ["dx://project-GJbvyPjJy3Gy01jz4x8bXzgv:/Bulk/Imputation/UKB\ imputation\ from\ genotype/ukb22828_c10_b0_v3.bgen","dx://project-GJbvyPjJy3Gy01jz4x8bXzgv:/Bulk/Imputation/UKB\ imputation\ from\ genotype/ukb22828_c6_b0_v3.bgen"]

Gvaihir commented 1 year ago

Where does it break - compile time or runtime? And add the error stack trace please.

nshrine commented 1 year ago

Where does it break - compile time or runtime? And add the error stack trace please.

At compile time, and I have fixed it, you just need to use "%20" instead of spaces i.e.:

Array[File]+ bgens = ["dx://project-GJbvyPjJy3Gy01jz4x8bXzgv:/Bulk/Imputation/UKB%20imputation%20from%20genotype/ukb22828_c10_b0_v3.bgen","dx://project-GJbvyPjJy3Gy01jz4x8bXzgv:/Bulk/Imputation/UKB%20imputation%20from%20genotype/ukb22828_c6_b0_v3.bgen"]

Gvaihir commented 1 year ago

Good:)