Fix nxf_date for uutils coreutils (Ubuntu 26.04+)

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>

Author: robsyme

modules/nextflow/src/main/resources/nextflow/executor/command-run.txt

@@ -30,15 +30,16 @@ nxf_sleep() {
 
 nxf_date() {
     ## should return the current timestamp in milliseconds
-    ## note1: some linux silently ignores the `%3N` option and returns the ts in seconds (len==10)
-    ## note2: old date tool ignores the `%3N` option and append that string to the timestamp in seconds
-    ## note3: mac date tools ignores the `%3N` option and the string `3N` is appended to the timestamp in seconds
-    local ts=$(date +%s%3N);
-    if [[ ${#ts} == 10 ]]; then echo ${ts}000
-    elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
-    elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
-    elif [[ ${#ts} == 13 ]]; then echo $ts
-    else echo "Unexpected timestamp value: $ts"; exit 1
+    ## handles GNU coreutils (9-digit %N), uutils coreutils (zero-stripped %N),
+    ## and BSD/macOS date (literal "N" from %N, falling back to second precision)
+    local s n
+    s=$(date +%s)
+    n=$(date +%N)
+    if [[ $n =~ ^[0-9]+$ ]]; then
+        n=$(printf '%09d' "$((10#$n))")
+        echo "$((s * 1000 + 10#${n:0:3}))"
+    else
+        echo "$((s * 1000))"
     fi
 }
 

modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt

@@ -207,12 +207,14 @@ nxf_sleep() {
 }
 
 nxf_date() {
-    local ts=$(date +%s%3N);
-    if [[ ${#ts} == 10 ]]; then echo ${ts}000
-    elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
-    elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
-    elif [[ ${#ts} == 13 ]]; then echo $ts
-    else echo "Unexpected timestamp value: $ts"; exit 1
+    local s n
+    s=$(date +%s)
+    n=$(date +%N)
+    if [[ $n =~ ^[0-9]+$ ]]; then
+        n=$(printf '%09d' "$((10#$n))")
+        echo "$((s * 1000 + 10#${n:0:3}))"
+    else
+        echo "$((s * 1000))"
     fi
 }
 

modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt

@@ -15,12 +15,14 @@ nxf_sleep() {
 }
 
 nxf_date() {
-    local ts=$(date +%s%3N);
-    if [[ ${#ts} == 10 ]]; then echo ${ts}000
-    elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
-    elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
-    elif [[ ${#ts} == 13 ]]; then echo $ts
-    else echo "Unexpected timestamp value: $ts"; exit 1
+    local s n
+    s=$(date +%s)
+    n=$(date +%N)
+    if [[ $n =~ ^[0-9]+$ ]]; then
+        n=$(printf '%09d' "$((10#$n))")
+        echo "$((s * 1000 + 10#${n:0:3}))"
+    else
+        echo "$((s * 1000))"
     fi
 }