alignments.fof

arcs/pipeline.sh

@@ -14,13 +14,15 @@ SERRAN_ASSEMBLY="/media/bigvol/peguerin/donnees/serran_genome_lgt3000.fasta"
 SERRAN_CHROMIUM_INTERLAVED="/media/bigvol/peguerin/xxx/outs/barcoded.fastq.gz"
 
 ## index genome assembly
-nohup bwa index $SERRAN_ASSEMBLY &
-
+bwa index $SERRAN_ASSEMBLY
+mv nohup.out index.log
 ## run alignments
-nohup bwa mem -t 48 $SERRAN_ASSEMBLY -p $SERRAN_CHROMIUM_INTERLAVED &
+bwa mem -t 48 $SERRAN_ASSEMBLY -p $SERRAN_CHROMIUM_INTERLAVED > aln_serran.sam
+mv nohup.out aln.log
 
-| samtools view -Sb - | samtools sort -n - ./CHROMIUM-sorted &
+samtools view -Sb aln_serran.sam | samtools sort -n -o aln_serran.sorted.bam - &
+echo "aln_serran.sorted.bam" > alignments.fof
 
 
 ##  Running ARCS...
-nohup ./ARCS.sh 5 0.05 30000 $SERRAN_ASSEMBLY &
\ No newline at end of file
+./ARCS.sh 5 0.05 30000 $SERRAN_ASSEMBLY
\ No newline at end of file