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Relative path in json files for cromwell

DivyKangeyanDivyKangeyan Member, Broadie
edited October 2018 in Ask the Cromwell + WDL Team

I have the following json file that has absolute path for all the files.

{
    "call_bismark_pool.r1_fastq": "/Users/Divy/Documents/dna-methylation-tools/testdata/small_01_R1.fastq.gz, /Users/Divy/Documents/dna-methylation-tools/testdata/small_02_R1.fastq.gz , /Users/Divy/Documents/dna-methylation-tools/testdata/small_03_R1.fastq.gz",
    "call_bismark_pool.r2_fastq": "/Users/Divy/Documents/dna-methylation-tools/testdata/small_01_R2.fastq.gz, /Users/Divy/Documents/dna-methylation-tools/testdata/small_02_R2.fastq.gz, /Users/Divy/Documents/dna-methylation-tools/testdata/small_03_R2.fastq.gz",
    "call_bismark_pool.chrom_sizes": "/Users/Divy/Downloads/mm10.chrom.sizes",
    "call_bismark_pool.monitoring_script": "/Users/Divy/Documents/dna-methylation-tools/monitor.sh",
    "call_bismark_pool.genome_index": "/Users/Divy/Documents/dna-methylation-tools/testdata/bismark_mm10_chr19.tar.gz",
    "call_bismark_pool.multicore": "1",
    "call_bismark_pool.memory": "24 GB",
    "call_bismark_pool.disks": "local-disk 100 SSD",
    "call_bismark_pool.cpu": 4,
    "call_bismark_pool.preemptible": 1,
    "call_bismark_pool.samplename": "sample-1"

}

It works fine with the absolute path but when I try to use the relative path it fails . This is how I specify the relative paths in json file

```
{
"call_bismark_pool.r1_fastq": "/dna-methylation-tools/testdata/small_01_R1.fastq.gz, /dna-methylation-tools/testdata/small_02_R1.fastq.gz , /dna-methylation-tools/testdata/small_03_R1.fastq.gz",
"call_bismark_pool.r2_fastq": "/dna-methylation-tools/testdata/small_01_R2.fastq.gz, /dna-methylation-tools/testdata/small_02_R2.fastq.gz, /dna-methylation-tools/testdata/small_03_R2.fastq.gz",
"call_bismark_pool.chrom_sizes": "../Downloads/mm10.chrom.sizes",
"call_bismark_pool.monitoring_script": "/dna-methylation-tools/monitor.sh",
"call_bismark_pool.genome_index": "/dna-methylation-tools/testdata/bismark_mm10_chr19.tar.gz",
"call_bismark_pool.multicore": "1",
"call_bismark_pool.memory": "24 GB",
"call_bismark_pool.disks": "local-disk 100 SSD",
"call_bismark_pool.cpu": 4,
"call_bismark_pool.preemptible": 1,
"call_bismark_pool.samplename": "sample-1"

}

Is it possible to specify relative paths in json file? If so what is the right way to specify it?

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