generating a simple NGS workflow with JSON, apache velocity and jsvelocity https://github.com/lindenb/jsvelocity

config.json

{
    "reference": {
        "name": "ref", 
        "fasta": "/path/to/ref.fasta"
    }, 
    "samples": [
        {
            "fastq": [
                "path/to/Sample1/Sample1_1.fq.gz", 
                "path/to/Sample1/Sample1_2.fq.gz"
            ], 
            "name": "Sample1"
        }, 
        {
            "fastq": [
                "path/to/Sample2/Sample2_1.fq.gz", 
                "path/to/Sample2/Sample2_2.fq.gz"
            ], 
            "name": "Sample2"
        }, 
        {
            "fastq": [
                "path/to/Sample3/Sample3_1.fq.gz", 
                "path/to/Sample3/Sample3_2.fq.gz"
            ], 
            "name": "Sample3"
        }
    ], 
    "tools": {
        "bcftools": "/path/to/bcftools", 
        "bwa": "/path/to/bwa", 
        "samtools": "/path/to/samtools"
    }
}

exectute.bash

java -jar jsvelocity.jar -f config config.json make.vm > Makefile

make.vm

REF=${config.reference.fasta}
.PHONY:all

all: align/variants.vcf

align/variants.vcf: #foreach($sample in ${config.samples}) align/${sample.name}_sorted.bam #end

	${config.tools.samtools} mpileup -uf ${REF}  $^  |\
	${config.tools.bcftools} view -vcg - >$@

#foreach($sample in ${config.samples})

align/${sample.name}_sorted.bam : ${sample.fastq[0]} ${sample.fastq[1]}
	mkdir -p $(dir $@) && \
	${config.tools.bwa} mem -R '@RG\tID:${sample.getId()}\tSM:${sample.name}'  ${REF} $^ |\
	${config.tools.samtools} view -b -S  - |\
	${config.tools.samtools} sort - $(basename $@) && \
	${config.tools.samtools} index $@

#end

Makefile

REF=/path/to/ref.fasta
.PHONY:all

all: align/variants.vcf

align/variants.vcf:  align/Sample1_sorted.bam  align/Sample2_sorted.bam  align/Sample3_sorted.bam 
	/path/to/samtools mpileup -uf ${REF}  $^  |\
	/path/to/bcftools view -vcg - >$@


align/Sample1_sorted.bam : path/to/Sample1/Sample1_1.fq.gz path/to/Sample1/Sample1_2.fq.gz
	mkdir -p $(dir $@) && \
	/path/to/bwa mem -R '@RG\tID:id10\tSM:Sample1'  ${REF} $^ |\
	/path/to/samtools view -b -S - |\
	/path/to/samtools sort - $(basename $@) && \
	/path/to/samtools index $@


align/Sample2_sorted.bam : path/to/Sample2/Sample2_1.fq.gz path/to/Sample2/Sample2_2.fq.gz
	mkdir -p $(dir $@) && \
	/path/to/bwa mem -R '@RG\tID:id15\tSM:Sample2'  ${REF} $^ |\
	/path/to/samtools view -b -S  - |\
	/path/to/samtools sort - $(basename $@) && \
	/path/to/samtools index $@


align/Sample3_sorted.bam : path/to/Sample3/Sample3_1.fq.gz path/to/Sample3/Sample3_2.fq.gz
	mkdir -p $(dir $@) && \
	/path/to/bwa mem -R '@RG\tID:id20\tSM:Sample3'  ${REF} $^ |\
	/path/to/samtools view -b -S - |\
	/path/to/samtools sort - $(basename $@) && \
	/path/to/samtools index $@