From e98e0e15d0d12fe0c020fa4f09093aedd42cbce9 Mon Sep 17 00:00:00 2001
From: Chloe Marie Loiseau <loiseau@login20.cluster.bc2.ch>
Date: Mon, 14 May 2018 23:14:13 +0200
Subject: [PATCH] changes to submission scripts

---
 notebooks/slurm_scripts/launch_BWA.slurm     | 2 +-
 notebooks/slurm_scripts/launch_bamqc.slurm   | 2 +-
 notebooks/slurm_scripts/launch_mpileup.slurm | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/notebooks/slurm_scripts/launch_BWA.slurm b/notebooks/slurm_scripts/launch_BWA.slurm
index 6fd419b..0484fca 100644
--- a/notebooks/slurm_scripts/launch_BWA.slurm
+++ b/notebooks/slurm_scripts/launch_BWA.slurm
@@ -1,7 +1,7 @@
 #!/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
diff --git a/notebooks/slurm_scripts/launch_bamqc.slurm b/notebooks/slurm_scripts/launch_bamqc.slurm
index 42919a9..c100118 100644
--- a/notebooks/slurm_scripts/launch_bamqc.slurm
+++ b/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
diff --git a/notebooks/slurm_scripts/launch_mpileup.slurm b/notebooks/slurm_scripts/launch_mpileup.slurm
index aca1de1..d737acc 100644
--- a/notebooks/slurm_scripts/launch_mpileup.slurm
+++ b/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
 
-- 
GitLab