Add -- to printf

[arnaudceol]

We are running nextflow in our instititute on a HPC cluster (pbspro). From time to time the the jobs fail with the following message:

Command wrapper:
  /var/spool/pbs/mom_priv/jobs/1746174.hpcfe01.SC: line 317: printf: -1: invalid option
  printf: usage: printf [-v var] format [arguments]

The error refers to the on_exit part of teh scripts:

on_exit() {
    exit_status=${nxf_main_ret:=$?}
    printf $exit_status > /scratch/work/b8/be8af4032f03985a745180e11b5b9d/.exitcode
    set +u
    [[ "$tee1" ]] && kill $tee1 2>/dev/null
    [[ "$tee2" ]] && kill $tee2 2>/dev/null
    [[ "$ctmp" ]] && rm -rf $ctmp || true
    rm -rf $NXF_SCRATCH || true
    sync || true
    exit $exit_status
}

There may be many reasons for the original error to occurs (almost all the time the pipeline calls samtools, it may also be related to some latency on our cluster).

Nevertheless it may be useful to protect the string given to printf in order to avoid errors at this step. It should be doable with by adding -- : printf -- $exit_status (see for instance https://unix.stackexchange.com/questions/22764/dashes-in-printf)

[pditommaso]

Issues solved in less than 4 hours! OSS is great!