Handling SIGPIPE error in snakemake

Question

The following snakemake script:

rule all:
    input:
        \'test.done\'

rule pipe:
   output:
       \'test.done\'
   shell:
        \"\"\"
        seq 1         


        

Answer 1

Yes, Snakemake sets pipefail by default, because in most cases this is what people implicitly expect. You can always deactivate it for specific commands by prepending set +o pipefail; to the shell command.