Merge pull request #51 from williamrowell/feature/sam-vcf-record-md5s…

…um-test

md5sum comparison of SAM or BCF records

src/wdlci/wdl_tests/calculate_sam_record_md5sum.wdl

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+version 1.0
+
+# Compare md5sums of SAM records in input files, e.g., BAMs or CRAMs while ignoring headers
+# Input type: SAM/BAM/CRAM
+
+task calculate_sam_record_md5sum {
+	input {
+		File current_run_output
+		File validated_output
+	}
+
+	Int disk_size = ceil(size(current_run_output, "GB") + size(validated_output, "GB") + 50)
+
+	command <<<
+		set -euo pipefail
+
+		err() {
+			message=$1
+
+			echo -e "[ERROR] $message" >&2
+		}
+
+		# Compare files
+		echo "Comparing SAM record md5sums"
+		current_run_md5sum=$(samtools view ~{current_run_output} | md5sum | cut -d ' ' -f 1)
+		validated_output_md5sum=$(samtools view ~{validated_output} | md5sum | cut -d ' ' -f 1)
+
+		if [[ "$current_run_md5sum" != "$validated_output_md5sum" ]]; then
+			err "SAM record md5sums did not match:
+				Expected md5sum: [$validated_output_md5sum]
+				Current run md5sum: [$current_run_md5sum]"
+			exit 1
+		else
+			echo "SAM record md5sums matched for file [~{basename(validated_output)}]"
+		fi
+	>>>
+
+	output {
+	}
+
+	runtime {
+		docker: "dnastack/dnastack-wdl-ci-tools:0.0.1"
+		cpu: 1
+		memory: "3.75 GB"
+		disk: disk_size + " GB"
+		disks: "local-disk " + disk_size + " HDD"
+		preemptible: 1
+	}
+}

src/wdlci/wdl_tests/calculate_vcf_record_md5sum.wdl

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+version 1.0
+
+# Compare md5sums of VCF records in input files, ignoring headers
+# Input type: VCF/BCF/VCF.gz/BCF.gz
+
+task calculate_vcf_record_md5sum {
+	input {
+		File current_run_output
+		File validated_output
+	}
+
+	Int disk_size = ceil(size(current_run_output, "GB") + size(validated_output, "GB") + 50)
+
+	command <<<
+		set -euo pipefail
+
+		err() {
+			message=$1
+
+			echo -e "[ERROR] $message" >&2
+		}
+
+		# Compare files
+		echo "Comparing VCF record md5sums"
+		current_run_md5sum=$(bcftools view -H ~{current_run_output} | md5sum | cut -d ' ' -f 1)
+		validated_output_md5sum=$(bcftools view -H ~{validated_output} | md5sum | cut -d ' ' -f 1)
+
+		if [[ "$current_run_md5sum" != "$validated_output_md5sum" ]]; then
+			err "VCF record md5sums did not match:
+				Expected md5sum: [$validated_output_md5sum]
+				Current run md5sum: [$current_run_md5sum]"
+			exit 1
+		else
+			echo "VCF record md5sums matched for file [~{basename(validated_output)}]"
+		fi
+	>>>
+
+	output {
+	}
+
+	runtime {
+		docker: "dnastack/dnastack-wdl-ci-tools:0.0.1"
+		cpu: 1
+		memory: "3.75 GB"
+		disk: disk_size + " GB"
+		disks: "local-disk " + disk_size + " HDD"
+		preemptible: 1
+	}
+}