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.

Answer 2

A somehow clunky solution is to append || true to the script. This will make the command always exit cleanly, which is not acceptable. To check whether the script actually succeded you can query the array variable ${PIPESTATUS[@]} to ensure it contains the expected exit codes:

This script is ok:

seq 1 10000 | head | grep 1 > test.done || true
echo ${PIPESTATUS[@]}
141 0 0

This is not ok:

seq 1 10000 | head | FOOBAR > test.done || true
echo ${PIPESTATUS[@]}
0