How to silent all print logs of processes?

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1

Hello there,
Is there a way to disable the logs that are printed on the screen in a nextflow run?

With all the messages/logs it gets difficult to see output from view()

for example, I’ve a process with script as:

vcf-readcount-annotator -o "vcf_counted.vcf" -s TUMOR ${consensus_vcf} ${bamreadcount_tsv} DNA

or

Rscript /data1/software/Rscripts/filterConsensusVCF_v2.R ${vcf_readcount_annotated_file}

How do I silent their logs on the terminal?

2

The view operator prints messages to stdout and to the .nextflow.log. By default, stdout/stderr from tasks are not echoed out to stdout or the .nextflow.log.

The only times stdout/err are printed to the Nextflow stdout are:

  1. When a task errors out and the tail of the logs are included in the error message, or
  2. When the debug directive (docs) is set to true.

Can you share an example (screenshot or code snippet) that shows the sort of output you are describing?