Add NFTest (#179)

* Add NFTest template

* Add paired test case

* Add paired test case config and YAML

* Add assertions

* Add VCF comparison script

* Update CHANGELOG

CHANGELOG.md

@@ -8,6 +8,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+### Added
+- NFTest test case
 
 ---
 

nftest.yml

@@ -0,0 +1,37 @@
+---
+global:
+  temp_dir: ./test/work
+  nf_config: test/global.config
+  remove_temp: true
+  clean_logs: true
+
+cases:
+  - name: test-call-gSNP-paired
+    message: Test call-gSNP pipeline with one normal and one tumor pair
+    nf_script: ./main.nf
+    nf_config: test/test-call-gSNP-paired.config
+    params_file: test/Illumina-paired.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143.g.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143.g.vcf.gz
+        script: test/assert-vcf.sh
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_indel.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_indel.vcf.gz
+        script: test/assert-vcf.sh
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_snv.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_snv.vcf.gz
+        script: test/assert-vcf.sh
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143.vcf.gz
+        script: test/assert-vcf.sh
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_VQSR-SNP-AND-INDEL.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_VQSR-SNP-AND-INDEL.vcf.gz
+        script: test/assert-vcf.sh
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24149.g.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24149.g.vcf.gz
+        script: test/assert-vcf.sh
+      - actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_genotype-count.tsv
+        expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_genotype-count.tsv
+        method: md5

test/Illumina-paired.yaml

@@ -0,0 +1,8 @@
+---
+patient_id: "NA24143"
+input:
+  BAM:
+    normal:
+      - "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam"
+    tumor:
+      - "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam"

test/assert-vcf.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+function md5_vcf {
+    zcat "$1" | grep -v "^##" | md5sum | cut -d ' ' -f 1
+}
+
+received=$(md5_vcf "$1")
+expected=$(md5_vcf "$2")
+
+if [ "$received" == "$expected" ]
+then
+    echo "VCF files are equal."
+    exit 0
+else
+    echo "VCF files are not equal" >&2
+    exit 1
+fi

test/global.config

@@ -0,0 +1,9 @@
+docker {
+    enabled = true
+
+    // Pass user's UID/GID and group IDs to Docker
+    uid_and_gid = "-u \$(id -u):\$(id -g)"
+    all_group_ids = "\$(for i in `id --real --groups`; do echo -n \"--group-add=\$i \"; done)"
+
+    runOptions = "${uid_and_gid} ${all_group_ids}"
+}

test/test-call-gSNP-paired.config

@@ -0,0 +1,49 @@
+// EXECUTION SETTINGS AND GLOBAL DEFAULTS
+
+// External config files import. DO NOT MODIFY THESE LINES!
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+
+// Inputs/parameters of the pipeline
+params {
+    dataset_id = 'IlluminaTest'
+    blcds_registered_dataset = false // if you want the output to be registered
+
+    // Set to false to disable the publish rule and delete intermediate files as they're no longer needed
+    // Disable this option for large input BAMs where /scratch space may not be sufficient
+    save_intermediate_files = false
+
+    // Whether to cache intermediate processes. Set to false by default
+    // To enable caching, uncomment this option and set to true
+    // cache_intermediate_pipeline_steps = false
+
+    // Target intervals to process for DNA panel/targeted sequencing samples
+    // For WGS, leave this field blank. The intervals will be extracted automatically from the reference dictionary
+    // For WXS/WES and targeted sequencing samples: provide path to targets in .list, .intervals, BED file, or VCF file format
+    // Defaults to WGS mode
+    intervals = ""
+
+    // Number of intervals to split into and any additional splitting arguments
+    scatter_count = 50
+    split_intervals_extra_args = ''
+
+    // Reference - Used here hg38 decoy version
+    // GATK requires the reference fasta to be accompanied by a .fai index and .dict dictionary associated with the fasta for fast random access
+    // These can be found in the same folder as the reference here: /hot/ref/reference/GRCh38-BI-20160721
+    reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
+
+    // GATK bundle - Used here hg38 decoy version
+    bundle_mills_and_1000g_gold_standard_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
+    bundle_v0_dbsnp138_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz"
+    bundle_hapmap_3p3_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz"
+    bundle_omni_1000g_2p5_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz"
+    bundle_phase1_1000g_snps_high_conf_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
+
+    // Base resource allocation updater
+    // See README for adding parameters to update the base resource allocations
+}
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()