I started using tag to identify the samples each process are processing and simultaneously I started losing visibility of the process names itself.
It turns out that the output width of a nextflow run is affected by the width of the terminal. That makes sense when the terminal is an interactive one, but when the output is redirected to a file, it makes no sense that it changes following the changes of the enclosing terminal.
Also, my production executions are triggered by a Jenkins server that connects to a slave in the HPC infrastructure. There is no terminal I can actuate on. But the output is reduced to some small number of columns, which causes me not to be able to clearly see what is happening (although the tag is now clearly visible).
Which is the way to tell Nextflow which is the desired width of the output?
I tried with export COLUMNS=200, but it didn’t worked
Are you using the -ansig-log false argument? This should not only solve the column width issue, but will also ensure that each task is printed to a separate line in the output.
For example:
nextflow run hello -ansi-log false
You may also find the .nextflow.log file useful as it also contains the full list of tasks the tags and the work directory paths (in addition to many other useful pieces of information).
No, I’m not using the -ansi-log argument, as this will change the functionality.
I’m interested in the standard tty output, where the processes are grouped by name and tell me how many are finished and how many are in total (with the completion percentage next to it). This gives me an overview of the whole execution.
Having just each task printed in the output is useless to me, as gives me no information on how the overall execution is going. If I’m interested in that kind of information, I can check the .nextflow.log file or the trace file.
My interest is in an overview of the whole situation, and for that I need the summary (not the individual processes information) and enough width to be able to know which process are we talking about. Right now, the tag is most of the view, so I don’t know if it is being preprocessed, aligned, indexed, or any other process.
