Fix nxf_date for uutils coreutils (Ubuntu 26.04+)#7118
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Fix nxf_date for uutils coreutils (Ubuntu 26.04+)#7118
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uutils coreutils ignores the %3N field-width modifier on `date` and strips leading zeros from %N, so `date +%s%3N` returns a variable-length string (11-19 digits) that no length branch in nxf_date matches. The function falls through to `exit 1`, which is swallowed by the `local var=$(...)` wrapper at the call site, leaving the caller with the literal error string. The next arithmetic expression then triggers "bash: line 178: Unexpected: unbound variable" under set -u and kills the task. Replace the length-dispatch implementation with a version that calls `date +%s` and `date +%N` separately, re-pads %N to 9 digits to recover any zeros uutils stripped, and computes milliseconds from the first three nanosecond digits. Falls back to second precision when %N is non-numeric (BSD/macOS), preserving existing behaviour on those platforms. Verified against both `ubuntu:latest` (uutils coreutils 0.8.0) and `ubuntu:24.04` (GNU coreutils 9.4): both produce 13-digit values with plausible non-negative wall-time deltas. Fixes #7114 Signed-off-by: Rob Syme <rob.syme@gmail.com>
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Summary
nxf_datefails on images using uutils coreutils (e.g.ubuntu:latest→ Ubuntu 26.04):Unexpected: unbound variableat.command.runline 178 #7114nxf_datepreviously useddate +%s%3Nand dispatched on output length to extract a 13-digit millisecond epoch. uutils coreutils (defaultdateon Ubuntu 26.04+) ignores the%3Nfield-width modifier and strips leading zeros from%N, producing a variable-length 11–19 digit string that hits no length branch and falls through toexit 1. The exit is swallowed by the surroundinglocal var=$(...), so callers get a literal error string assigned tostart_millis/end_millis; the next arithmetic expansion then aborts underset -uwithbash: line 178: Unexpected: unbound variable, killing the task.date +%sanddate +%Nseparately, re-pads%Nto 9 digits to recover any zeros uutils stripped, and computes milliseconds from the first three nanosecond digits. Non-numeric%N(BSD/macOS, where%Nreturns literalN) falls back to second precision, matching prior behaviour on those platforms.Test plan
:nextflow:test --tests BashWrapperBuilderTestpasses after fixture updatesubuntu:latest(uutils coreutils 0.8.0): produces 13-digit value with non-negative deltaubuntu:24.04(GNU coreutils 9.4): produces 13-digit value with non-negative delta