changes to submission scripts

notebooks/slurm_scripts/launch_BWA.slurm

 #!/bin/bash 
 
 #SBATCH --job-name=BWA
-#SBATCH --cpus-per-task=1
+#SBATCH --cpus-per-task=2
 #SBATCH --mem-per-cpu=4G
 #SBATCH --output=BWA.o
 #SBATCH --error=BWA.e

notebooks/slurm_scripts/launch_bamqc.slurm

@@ -4,4 +4,4 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
 
-singularity exec /home/container.img qualimap bamqc -bam ERR760779.dedup.realigned.bam -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc
+singularity exec /home/container.img qualimap bamqc -bam ERR760779.dedup.bam  -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc

notebooks/slurm_scripts/launch_mpileup.slurm

@@ -4,5 +4,5 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
 
-singularity exec /home/container.img samtools mpileup -ABQ0 -q 20 -f ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779.dedup.realigned.bam > ERR760779.pileup
+singularity exec /home/container.img samtools mpileup -ABQ0 -q 20 -f ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779.dedup.bam > ERR760779.pileup