Adds sbatch scripts for Escape_Variants.md steps 3-5

[johnbradley]

Adds changes to run the following steps from Escape_Variants.md

• 3. Map using BWA with the cleaned libraries
• 4. Create BAM from SAM and make an index
• 5. Create a dictionary file for using picard tools

Adds sbatch-array.sh script to simplify escape-variants-pipeline.sh. This script runs a sbatch array job appropriate for a file containing a list of filenames to process.

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For all module load commands without specific versions I am adding the default version. This is for better reproducibility.

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The Create BAM from SAM and make an index was using the [-N/--nodes] argument to specify one node:

#SBATCH -N 1

I removed that line because I didn't think it was having any effect.

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The Create a dictionary file for using picard tools step creates a MT246667.dict file. This step cannot be run twice without deleting the MT246667.dict file first. So subsequent runs of the pipeline will fail if this file is not deleted. This problem will be fixed as part of issue #3.

[johnbradley]

As of now the pipeline looks like this:

./run-escape-variants.sh
       `-> scripts/escape-variants-pipeline.sh
                    `-> scripts/index-reference-genome.sh
                    `-> scripts/remove-nextera-adapters.sh
                    `-> scripts/map-bwa-cleaned-libs.sh
                    `-> scripts/create-bam-from-sam.sh
                    `-> scripts/create-picard-dictionary.sh