Nextflow: how to obtain two files as outputs?

Question

I´m trying to write a small Nextflow pipeline that takes three inputs and gives two outputs: a .log.weir.fst and a .log file. When i run the pipeline, it only gives the .log.weir.fst files but not the .log files. I tried running "bash .command.sh" in the work directory to see if my code is wrong, but the code actually generates the two files in the working directory. I appreciate any help.

Answer 1

Without the code of how you define the process, it's very difficult to know what is wrong. Please consider adding it to your question. When posting consider showing some of your code and aim for people to be able to reproduce your problem.

A first response could be to look at the output block and make sure that both files are listed as outputs of your process. My guess is that this is not done and therefore your log.weir.fst file is buried inside the work directory because Nextflow is designed to only show you relevant files and not the intermediates. use find ./work -name '*log.weir.fst*' to see if this is the case.

As a tip: you can have more than one line of output definitions in the block.

To understand this better please see: https://www.nextflow.io/docs/latest/process.html#multiple-output-files https://www.nextflow.io/docs/latest/process.html#publishdir