Update scripts

build_singularity.sh

@@ -1,13 +1,15 @@
 #!/usr/bin/env bash
 #
 # Title: build_signularity.sh
-# Description:
-# Usage:
+# Description: This script builds a Singularity image from a docker image.
+# Usage: ./build_signularity.sh [with_references]
 # Date Created: 2023-01-11 13:28
-# Last Modified: Tue 24 Jan 2023 10:00:57 AM EST
+# Last Modified: Mon 18 Dec 2023 05:19:33 PM EST
 # Author: Reagan Kelly ([email protected])
 #
 
+
+# NOTE: The "SINGULARITY_TMPDIR=~/.tmp" is only required if your system has "noexec" set on the /tmp mount
 if [[ ${1} == 'with_references' ]]; then
     echo 'Building singularity image with references included'
     SINGULARITY_TMPDIR=~/.tmp singularity build pipeline_with_references.sif docker://ghcr.io/cdcgov/varpipe_wgs_with_refs:latest

get_gatk.sh

@@ -1,19 +1,19 @@
 #!/bin/bash
 #
 # Title: get_gatk.sh
-# Description:
-# Usage:
+# Description: Retrieves GATK for the pipeline to use
+# Usage: Used by setup.sh
 # Date Created: 2023-01-23 14:30
-# Last Modified: Wed 25 Jan 2023 10:02:39 AM EST
+# Last Modified: Mon 18 Dec 2023 05:22:54 PM EST
 # Author: Reagan Kelly ([email protected])
 #
 
 DL_URL='https://github.com/broadinstitute/gatk/releases/download/4.2.4.0/gatk-4.2.4.0.zip'
 
 mkdir tmp
-cd tmp
+pushd tmp
 wget -O- $DL_URL >gatk-4.2.4.0.zip
 unzip gatk-4.2.4.0.zip
 mv gatk-4.2.4.0/gatk-package-4.2.4.0-local.jar ../tools/gatk-4.2.4.0/
-cd ../
+popd
 rm -rf tmp/

tools/clockwork-0.11.3/OUT/build_references.sh

@@ -1,15 +1,17 @@
 #!/usr/bin/env bash
 #
 # Title: build_references.sh
-# Description:
-# Usage:
+# Description: Combines the downloaded reference files and creates a BWA index
+# Usage: Used by setup.sh
 # Date Created: 2023-01-23 20:21
-# Last Modified: Mon 23 Jan 2023 08:26:17 PM EST
+# Last Modified: Mon 18 Dec 2023 05:24:54 PM EST
 # Author: Reagan Kelly ([email protected])
 #
 
 gunzip ref.??.fa.gz
 
 cat ref.??.fa >ref.fa
 
+rm ref.??.fa
+
 ../../bwa index -b 100000000 ref.fa