Hi, I'm trying to fix an small undeterministic table for

TAXPASTA/MERGE

. I tried to use

path(process.out.merged_profiles[0][1])
                        .csv(sep: "\t")
                        .sortRows()
                        .sortColumns()

But the output is still unordered. Is there something wrong with my command ?

Depending on the input data, it could be that some mof the numbers might be a bit different

You can find it here: https://github.com/nf-core/modules/pull/10076

OPk yeah it's using kraken2

The issue is more than on Conda the line order is correct but not on docker and singularity 😕

OH I see!

You can find the difference here: https://github.com/nf-core/modules/actions/runs/22110615963/job/63905830637?pr=10076

Oh I see... so the

sortRows

isn't working consistently between nf-test conda/docker runs?!

I guess it's more that

sortRows

doesn't work at all. The output is already ordered in conda and not in containers.

Understood

It seems to be a problem in nft-csv

public TableWrapper sortRows() { 
     List<Column<?>> columns = table.columns(); 
     String[] columnNames = columns.stream().map(Column::name).toArray(String[]::new); 
     table.sortOn(columnNames); 
     return this; 
 }

this

is not updated to the new sorted table.

🎉