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Updating tools/bwameth from version 0.2.6 to 0.2.7 #5262

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optimize samtools
bgruening authored May 19, 2024
commit 184f4027ed8cb939a0a8fd28e00b6741b6fc2ea4
3 changes: 2 additions & 1 deletion tools/bwameth/bwameth.xml
Original file line number Diff line number Diff line change
@@ -78,7 +78,8 @@ bwameth.py
#else:
$read1 $read2
#end if
| samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
| samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o output.bam
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Please undo this change and maybe add the explanation from here

## Convert SAM output to sorted BAM

Maybe use exactly the command line from over there:

| samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o output.bam


]]></command>
<inputs>
<conditional name="referenceSource">