config.yaml

{
"samples":['sample_1','samples_2','samples_160','sample_161'],
"references": ['UCD','Angus'],
    "resources":{
        "raw":"/path/to/fastq/",
        "reference":"/path/to/ref/genome/"
    },
    "tools":{
        "fastp":"/path/to/software/fastp",
        "load_python_374":"module load python_gpu/3.7.4 \n",
        "load_bwa":"module load bwa/0.7.17 \n",
        "load_samtools":"module load samtools/1.6 \n",
        "fastq_splitter":"/path/to/software//gdc-fastq-splitter/venv/bin/gdc-fastq-splitter",
        "samblaster":"/path/to/software//samblaster/samblaster",
        "sambamba":"/path/to/software//sambamba_v0.6.6",
        "load_picard_tools":"module load picard/2.18.17 \n",
        "load_java_jdk":"module load jdk \n",
        "load_r":"module load r/3.6.1 \n",
        "picard_tools":"java -jar /path/to/software//gcc-4.8.5/picard-2.18.17-jiviugfnvhk4qlzbcugx6bpzixgb7znb/bin/picard.jar",
        "sam_flags_script":"bash path/to/software/MQ_sam_reads.sh ",
    },
    "fold_out":{
        "fastp":"/path/output/fastp/",
        "split_fastq":"/path/output/split_fastq/",
        "alignment":"/path/output/alignment/",
        "sorted_alignment":"/path/output/sorted_alignment/",
        "dedup_alignment":"/path/output/dedup_alignment/",
        "picard_metrics":"/path/output/Picard_metrics/",
        "map_stats":"/path/output/mapping_stats/"
    }
}