diff --git a/tools/bwameth/bwameth.xml b/tools/bwameth/bwameth.xml index f1ccad9e3c4..60375139e7f 100644 --- a/tools/bwameth/bwameth.xml +++ b/tools/bwameth/bwameth.xml @@ -1,7 +1,7 @@ Fast and accurate aligner of BS-Seq reads. - 0.2.6 + 0.2.7 bwameth @@ -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 -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o output.bam + ]]> @@ -153,7 +154,7 @@ bwameth.py **What it does** -BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool. +BWA-meth performs the alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. This methodology is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool. ]]> @misc{1401.1129,