paths in scripts

notebooks/slurm_scripts/launch_BWA.slurm

@@ -13,7 +13,7 @@ singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/referenc
 
 singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1U.trimmed.fastq.gz > ERR760779_1U.sam
 
-singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_refe/home/rence.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam
+singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam
 
 ### convert the SAM to BAM format
 singularity exec /home/container.img samtools view -bhu ERR760779_paired.sam > ERR760779_paired.bam
@@ -23,7 +23,7 @@ singularity exec /home/container.img samtools view -bhu ERR760779_2U.sam > ERR76
 ### sort the BAM file by position
 singularity exec /home/container.img samtools sort -m 4G ERR760779_paired.bam > ERR760779.sorted.bam
 singularity exec /home/container.img samtools sort -m 4G ERR760779_1U.bam > ERR760779_1U.sorted.bam
-singularity exec container.img samtools sort -m 4G ERR760779_2U.bam > ERR760779_2U.sorted.bam
+singularity exec /home/container.img samtools sort -m 4G ERR760779_2U.bam > ERR760779_2U.sorted.bam
 
 ### To go faster one could bring the three last commands into one using pipe:
 ### bwa mem -t 2 -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz | samtools view -Sbhu -|samtools sort -m 4G - ERR760779_paired.sorted

notebooks/slurm_scripts/launch_bamqc.slurm

@@ -2,6 +2,6 @@
 
 #SBATCH --job-name=bamQC
 #SBATCH --cpus-per-task=1
-#SBATCH --mem-per-cpu=2G
+#SBATCH --mem-per-cpu=4G
 
 singularity exec /home/container.img qualimap bamqc -bam ERR760779.dedup.bam -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc

notebooks/slurm_scripts/launch_snpeff.slurm

@@ -4,4 +4,4 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
 
-singularity exec /home/container.img snpEff ann -c ~/Workshop_SA/notebooks/annotation/snpEff.config -noStats -no-downstream -no-upstream MTB_ANC -interval ~/Workshop_SA/notebooks/annotation/additionnal_annotations.bed ERR760779.snps.vcf > ERR760779.snps.ann.vcf
+singularity exec /home/container.img snpEff ann -c /home/Workshop_SA/notebooks/annotation/snpEff.config -noStats -no-downstream -no-upstream MTB_ANC -interval ~/Workshop_SA/notebooks/annotation/additionnal_annotations.bed ERR760779.snps.vcf > ERR760779.snps.ann.vcf

notebooks/slurm_scripts/launch_trimmomatic.slurm

 #!/bin/bash 
 
 #SBATCH --job-name=trimmomatic
-#SBATCH --cpus-per-task=1
+#SBATCH --cpus-per-task=2
 #SBATCH --mem-per-cpu=4G
 #SBATCH --output=trimmomatic.o
 #SBATCH --error=trimmomatic.e
 
 
-singularity exec /home/container.img trimmomatic PE -phred33  ~/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz  ~/Workshop_SA/data_Eldholm/ERR760779_2.fastq.gz ERR760779_1P.trimmed.fastq.gz ERR760779_1U.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz ERR760779_2U.trimmed.fastq.gz ILLUMINACLIP:~/Workshop_SA/notebooks/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:20
+singularity exec /home/container.img trimmomatic PE -phred33 -threads 2 $HOME/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz  $HOME/Workshop_SA/data_Eldholm/ERR760779_2.fastq.gz ERR760779_1P.trimmed.fastq.gz ERR760779_1U.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz ERR760779_2U.trimmed.fastq.gz ILLUMINACLIP:$HOME/Workshop_SA/notebooks/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:20