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Resolve the BWA index prefix without find(1) #95

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Resolve the BWA index prefix without find(1) #95

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15 changes: 14 additions & 1 deletion modules/local/bamprocessing/merge_align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,20 @@ process MERGE_ALIGN {
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
# The BWA index prefix, resolved with a glob and bash parameter expansion instead of `find`.
# Seqera Containers builds the Docker image of a conda spec on an Ubuntu base but the
# Singularity image on an Amazon Linux 2023 one, and that base ships no findutils, so the usual
# `find -L ./ -name "*.amb"` fails with exit 127 under -profile singularity. Globbing needs no
# external binary. The leading ./ is kept so the prefix, which bwa records in the BAM's @PG
# header, stays exactly what find returned.
INDEX=''
for amb in ./${index}/*.amb; do
if [ -e "\$amb" ]; then INDEX="\${amb%.amb}"; fi
done
if [ -z "\$INDEX" ]; then
echo "No BWA index (*.amb) found in './${index}'" >&2
exit 1
fi

# Merge the overlapping mates of each raw read pair into one consensus read, so the overlap is
# counted once and its bases carry a recalculated quality. Merging comes first, before any
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