How to define a specific error message when checkIfExists of fromPath is failed

[liuyang2006]

Dear Nextflow,
I want my pipeline show a specific error message that can help the users when the statement is not passed: genome_ch = Channel.fromPath(genome_path, type: 'any', checkIfExists: true) , however, I could not found how to achieve this. Would you please help me to find a way? Thank you very much!

Running command:

nextflow run TheJacksonLaboratory/nanome \
      --input https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz\
       --dsname Test --genome hg1234

Error message now:

No such file: /gpfs/ctgs0/fastscratch/liuya/nanome/test/hg1234

I want to change the error message to my specific message in order to tell users more information. Thank you!

[manuelesimi]

Hello,

You could check yourself if the path exists and return a custom message with the following code:

genome_path = file(genome_path)
if ( !genome_path.exists() )
    exit 1, "Genome path does not exist"

genome_ch = Channel.fromPath(genome_path, type: 'any')

Thanks,
manuele

[liuyang2006]

Thank you! This solution can solve my problem.