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Replace sambamba with samtools for merge, view, flagstat in contamination analysis #15

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Replace sambamba with samtools for merge, view, flagstat in contamination analysis #15

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8 changes: 4 additions & 4 deletions workflow/rules/F_cont_analysis.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -1227,8 +1227,8 @@ rule F05_map_reads_for_blob:
done

echo "[GEP2] Merging $PAIR_IDX partial BAMs..."
sambamba merge \
-t {threads} \
samtools merge \
-@ {threads} \
{output.bam} \
"${{PARTIAL_BAMS[@]}}"

Expand All @@ -1251,13 +1251,13 @@ rule F05_map_reads_for_blob:
echo "[GEP2] BAM size: $((BAM_SIZE / 1024 / 1024)) MB"

# Quick validation: check BAM header
if ! sambamba view -H {output.bam} > /dev/null 2>&1; then
if ! samtools view -H {output.bam} > /dev/null 2>&1; then
echo "[GEP2] ERROR: Output BAM file is not valid" >&2
exit 1
fi

# Count mapped reads
MAPPED=$(sambamba flagstat -t {threads} {output.bam} 2>/dev/null | head -1 | awk '{{print $1}}')
MAPPED=$(samtools flagstat -@ {threads} {output.bam} 2>/dev/null | head -1 | awk '{{print $1}}')
echo "[GEP2] Total alignments: $MAPPED"

echo "[GEP2] Read mapping complete: {output.bam}"
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