fix seqtk module

align_nonhuman.sh

@@ -23,9 +23,7 @@
 
 set -e
 
-seqtk=/scratch/er01/apps/seqtk/seqtk #Compiled for Gadi
-
-# align_split.sh for non-human samples
+# align.sh for non-human samples
 
 ref=
 outdir=../Align_split
@@ -51,50 +49,7 @@ err=${errdir}/${outPrefix}.err
 
 echo fqpair:$fqpair fq1:$fq1 fq2:$fq2 sampleID:$sampleID centre:$centre lib:$lib platform:$platform flowcell:$flowcell lane:$lane outPrefix:$outPrefix err:$err ref:$ref NCPUS:$NCPUS
 
-$seqtk mergepe $fq1 $fq2 | bwa mem -p -t $NCPUS \
-        -R "@RG\tID:${flowcell}.${lane}_${sampleID}_${lib}\tPL:${platform}\tPU:${flowcell}.${lane}\tSM:${sampleID}\tLB:${sampleID}_${lib}\tCN:${centre}" \
-        -M ${ref} - 2> ${logdir}/${outprefix}.log.bwamem \
-        | samtools sort -n -@ $NCPUS -o ${outdir}/${outPrefix}.aln.bam
-
-if ! samtools quickcheck ${outdir}/${outPrefix}.aln.bam
-then
-        printf "Corrupted or missing BAM\n" > $err
-fi
-
-[gs5517@gadi-login-01 Scripts]$ cat align_nonhuman.sh
-#!/bin/bash
-
-set -e
-
-seqtk=/scratch/er01/apps/seqtk/seqtk #Compiled for Gadi
-
-# align_split.sh for non-human samples
-
-ref=./Reference/canFam4.fasta
-outdir=../Align_split
-logdir=Logs/Align
-errdir=Logs/Align_error_capture
-
-fqpair=`echo $1 | cut -d ',' -f 1`
-fq1=$(ls ${fqpair}*R1.f*q.gz) #Must check regex for each batch
-fq2=$(ls ${fqpair}*R2.f*q.gz)
-sampleID=`echo $1 | cut -d ',' -f 2`
-centre=`echo $1 | cut -d ',' -f 3`
-lib=`echo $1 | cut -d ',' -f 4`
-platform=`echo $1 | cut -d ',' -f 5`
-flowcell=`echo $1 | cut -d ',' -f 6`
-lane=`echo $1 | cut -d ',' -f 7`
-
-outPrefix=$(basename $fqpair)
-err=${errdir}/${outPrefix}.err
-
-#bwakit emits default sort order (queryname, but no SO tag in headers) or option to sort
-#by coordinate with samtools but does not allow the -n flag to specify sort order by name.
-#Sambamba requires queryname sorted with SO tag. Below code does it by force.
-
-echo fqpair:$fqpair fq1:$fq1 fq2:$fq2 sampleID:$sampleID centre:$centre lib:$lib platform:$platform flowcell:$flowcell lane:$lane outPrefix:$outPrefix err:$err ref:$ref NCPUS:$NCPUS
-
-$seqtk mergepe $fq1 $fq2 | bwa mem -p -t $NCPUS \
+seqtk mergepe $fq1 $fq2 | bwa mem -p -t $NCPUS \
         -R "@RG\tID:${flowcell}.${lane}_${sampleID}_${lib}\tPL:${platform}\tPU:${flowcell}.${lane}\tSM:${sampleID}\tLB:${sampleID}_${lib}\tCN:${centre}" \
         -M ${ref} - 2> ${logdir}/${outprefix}.log.bwamem \
         | samtools sort -n -@ $NCPUS -o ${outdir}/${outPrefix}.aln.bam