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Fix Cromwell submit-docker: remove the brace group that truncated the command #193

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Merged
kennedydane merged 1 commit into from
Oct 2, 2026
Merged

Fix Cromwell submit-docker: remove the brace group that truncated the command #193

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10 changes: 9 additions & 1 deletion ansible/roles/compiled/templates/cromwell_slurm.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,10 @@ backend {
# pull the image once into the user's Singularity cache, then run the task
# inside it. Bash variables are written bare ($IMAGE), never with braces:
# Cromwell interpolates the braced form itself before bash sees the script.
# Cromwell also wraps this string in a WDL command block, which the first
# closing brace that does not end one of its own references terminates
# ("Unrecognized token: sbatch"). So no bash brace groups or brace expansion
# anywhere in the string, shell comments included: use if/fi instead.
submit-docker = """
# Cache pulled images per user, on scratch rather than quota-limited $HOME.
if [ -z "$SINGULARITY_CACHEDIR" ]; then
Expand Down Expand Up @@ -67,7 +71,11 @@ backend {
&& mv $IMAGE.tmp $IMAGE \
&& echo "successfully pulled ${docker}!"
fi
) 9>$LOCK_FILE || { echo "Failed to pull ${docker}" >&2; exit 1; }
) 9>$LOCK_FILE
if [ $? -ne 0 ]; then
echo "Failed to pull ${docker}" >&2
exit 1
fi

# Submit the script to SLURM. `singularity` here and above comes from the
# unversioned `singularity` module that cromwell.lua loads; sbatch exports
Expand Down
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