Issues with StageIn fromFilePairs

[fgualdr]

Hi!,

I'm having issues figuring out a bug within my code. While I produce a file_pair channel using the Channel.fromFilePairs al follow:

"ch_fastq_file_path = Channel.fromFilePairs( params.fastq_file_path + '/*.R{1,2}.fastq.gz',checkIfExists:true) "

When giving this to a process called MAP that takes in as input the tuple: input: tuple val(sample_id), path(reads)

if I println the reads within the workflow I get as expected the full path while when println within the process I get only the base name and the mapping process fails as it does not find the files. Have to specify that I specified within the process the Staging mode: stageInMode 'symlink' stageOutMode 'copy'

So I would expect a symlink within the work directory but it doesn't.

Thanks for the help

Francesco