Added additional test scripts

tests/scripts/bqsr_identity_check.sh

+#!/bin/bash
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=10GB
+#SBATCH --time=48:00:00
+#SBATCH --job-name=bqsr_test
+#SBATCH --output=bqsr_test.out
+#SBATCH --error=bqsr_test.err
+
+SAMTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/bin/samtools
+
+#The outputs of bcbio and nf-core bqsr initially appear different
+#However, this can be accounted for by arbitrary ordering of reads with identical coordinates
+#They can be made identical by a sort operation - samtools sort is not suitable as they are already adequately sorted by samtools' definition
+
+#First, convert to sam
+
+#bcbio recal bam
+$SAMTOOLS view 158063_519317-sort-recal.bcbio.bam > 158063_519317-sort-recal.bcbio.sam
+
+#nf-core recal bam
+$SAMTOOLS view 158063_519317-recal.nf-core.bam > 158063_519317-recal.nf-core.sam
+
+#Sort the sam files using bash sort to confirm that they are indentical
+sort 158063_519317-recal.nf-core.sort.sam > 158063_519317-recal.nf-core.bashsort.sam 
+sort 158063_519317-sort-recal.bcbio.sort.sam > 158063_519317-sort-recal.bcbio.bashsort.sam  
+
+#Generate md5sums - these should be identical
+md5sum 158063_519317-recal.nf-core.bashsort.sam > 158063_519317-recal.nf-core.bashsort.sam.md5
+md5sum 158063_519317-sort-recal.bcbio.bashsort.sam > 158063_519317-sort-recal.bcbio.bashsort.sam.md5
+
+

tests/scripts/bwa_mem_identity_check.sh

+#!/bin/bash
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=10GB
+#SBATCH --time=24:00:00
+#SBATCH --job-name=bwa_identity
+#SBATCH --output=bwa_identity.out
+#SBATCH --error=bwa_identity.err
+
+SAMTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/bin/samtools
+
+#We know that running bwa mem multiple times on identical input produces identical output
+#We also wish to test that the nextflow and bcbio pipeline produce identical bam files when provided with identical fastqs
+#In this example, nextflow is run with the trimmed fastqs produced by the bcbio pipeline (via fastp)
+#We now wish to test that the resulting bam files are identical following bamsormadup (sort and mark duplicates)
+
+#Convert bams to sam - remove read group tags as naming convention differs slightly between pipelines
+
+#bcbio bam
+$SAMTOOLS view -x RG 158063_519317-sort.bam > 158063_519317-sort.noRG.sam
+
+#nextflow bam
+$SAMTOOLS view -x RG 158063.bam > 158063.noRG.sam
+
+#Generate md5sums - these should be identical
+md5sum 158063_519317-sort.noRG.sam > 158063_519317-sort.noRG.sam.md5
+md5sum 158063.noRG.sam > 158063.noRG.sam.md5
+
+

tests/scripts/bwa_stochasticity_check.sh

@@ -9,6 +9,10 @@
 BWA=/home/u035/u035/shared/software/bcbio/anaconda/bin/bwa
 SAMTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/bin/samtools
 
+#Is bwa mem deterministic - i.e. will it produce the same alignment given identical commands and input
+#The script below is designed to test this (the answer is 'yes')
+
+
 #Point to appropriate bwa index
 #In the pipeline, a softlink to this would be provided in the working directory
 INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`