These are chat archives for nextflow-io/nextflow
Is there a good way to avoid the output file "is out of the scope of process working dir” exception? I have a tool that has to write a file to a specific path outside of the working directory, and I need to use this file downstream in the Nextflow script.
My current solution is to create a hard link to this external location within the working directory and then use that version of the file, but this is extra boiler plate code that I’d rather avoid.
Nextflow seems like it should be able to handle it, except for these assertions https://github.com/nextflow-io/nextflow/blob/master/src/main/groovy/nextflow/script/ParamsOut.groovy#L469
storeDirwill allow me to move an output file from the working directory to another directory, but my problem is I’m using a tool that writes to a specific external path directly, and I want to capture it as an output for use in a subsequent channel.
mv /your/tool/abs/path $PWD
lninstead, but it’d be easier to maintain if I didn’t have to, as I have to leave a comment every time explaining why it’s done that way for other team members.
all pending jobs are killed except the jobs that are already running
scancel <job id>to kill a running job, can you confirm that's working in your cluster ?
executor. submitRateLimit = '<rate>'to reduce it