typo fgbio

alignment/markdups.sh

@@ -56,8 +56,8 @@ elif [ $algo == 'fgbio_umi' ]
 then
     module load fgbio bwa/intel/0.7.15
     samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
-    fgbio GroupReadsByUmi --tmp-dir ./ -s identity -i ${sbam} -o ${pair_id}.group.bam --family-size-histogram ${pair_id}.umihist.txt -e 0 -m 0
-    fgbio CallMolecularConsensusReads --tmp-dir ./ -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
+    fgbio --tmp-dir ./ GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam --family-size-histogram ${pair_id}.umihist.txt -e 0 -m 0
+    fgbio --tmp-dir ./ CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
     samtools index ${pair_id}.consensus.bam
     samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${pair_id}.consensus.bam
     gzip ${pair_id}.consensus.R1.fastq