Hi, In nf-core/phaseimpute we output some samplesheet to be use in latter step with the full path to the file produced, such as:

panel,chr,file
1000GP,chr21,/home/../.nf-test/tests/e6e20dcb71bf3b994064ab10d01e1a68/output/prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt
1000GP,chr22,/home../.nf-test/tests/e6e20dcb71bf3b994064ab10d01e1a68/output/prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt

The issue I have is that the md5sum of the csv change between local and GA execution. Should I ignore the csv for the nf-test or should I change to a relative path ? What is currently done in other pipeline ?

you can actually use nft-csv and make the proper assertions I believe