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Commit 8a242160 authored by Peter van 't Hof's avatar Peter van 't Hof
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fix on test file

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flexiprep/examples/test.json
+ 4
− 4
View file @ 8a242160
{
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"gatk": {"flexiprep": { "sdfg": { "exe": "gatk" }}},
"pbzip2": { "exe": "/home/pjvan_thof/pipelines/test/test" },
"pbzip2": { "exe": "test" },
"flexiprep": {
"fastqc": { "exe": "/home/pjvan_thof/pipelines/test/test" },
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
"fastqc": { "exe": "test" },
"cutadapt": {"exe":"test"},
"sickle": {"exe":"test"}
}
}
gatk/gatk-old/examples/test.json
+ 14
− 14
View file @ 8a242160
{
"samtools": { "exe": "test"},
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"star" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
"bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
"star" : {"exe":"test"},
"bwa" : {"exe":"test"},
"flexiprep": {
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
"fastqc": {"exe":"test"},
"sickle": {"exe":"test"}
},
"mapping": {
},
......@@ -15,30 +15,30 @@
}
},
"referenceFile" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "/home/pjvan_thof/pipelines/test/test",
"hapmap": "/home/pjvan_thof/pipelines/test/test",
"omni": "/home/pjvan_thof/pipelines/test/test",
"1000G": "/home/pjvan_thof/pipelines/test/test",
"mills": "/home/pjvan_thof/pipelines/test/test",
"dbsnp": "test",
"hapmap": "test",
"omni": "test",
"1000G": "test",
"mills": "test",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
}
},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"test"},
"samples": {
"test": {
"ID": "test",
"runs": {
"1" : {
"ID": "1",
"R1" : "/home/pjvan_thof/pipelines/test/test.R1.fastq.gz",
"R2" : "/home/pjvan_thof/pipelines/test/test.R2.fastq.gz"
"R1" : "test.R1.fastq.gz",
"R2" : "test.R2.fastq.gz"
},
"2" : {
"ID": "1",
"R1" : "/home/pjvan_thof/pipelines/test/test.R1.fastq.gz",
"R2" : "/home/pjvan_thof/pipelines/test/test.R2.fastq.gz"
"R1" : "test.R1.fastq.gz",
"R2" : "test.R2.fastq.gz"
}
}
}
......
gatk/gatk-pipeline/examples/test.json
+ 14
− 14
View file @ 8a242160
......@@ -3,11 +3,11 @@
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"samtools": { "exe": "test"},
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"star" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
"bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
"star" : {"exe":"test"},
"bwa" : {"exe":"test"},
"flexiprep": {
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
"fastqc": {"exe":"test"},
"sickle": {"exe":"test"}
},
"mapping": {
},
......@@ -17,30 +17,30 @@
}
},
"referenceFile" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "/home/pjvan_thof/pipelines/test/test",
"hapmap": "/home/pjvan_thof/pipelines/test/test",
"omni": "/home/pjvan_thof/pipelines/test/test",
"1000G": "/home/pjvan_thof/pipelines/test/test",
"mills": "/home/pjvan_thof/pipelines/test/test",
"dbsnp": "test",
"hapmap": "test",
"omni": "test",
"1000G": "test",
"mills": "test",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
}
},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"test"},
"samples": {
"test": {
"ID": "test",
"runs": {
"1" : {
"ID": "1",
"R1" : "/home/pjvan_thof/pipelines/test/test.R1.fastq.gz",
"R2" : "/home/pjvan_thof/pipelines/test/test.R2.fastq.gz"
"R1" : "test.R1.fastq.gz",
"R2" : "test.R2.fastq.gz"
},
"2" : {
"ID": "1",
"R1" : "/home/pjvan_thof/pipelines/test/test.R1.fastq.gz",
"R2" : "/home/pjvan_thof/pipelines/test/test.R2.fastq.gz"
"R1" : "test.R1.fastq.gz",
"R2" : "test.R2.fastq.gz"
}
}
}
......
mapping/examples/test.json
+ 3
− 3
View file @ 8a242160
......@@ -4,9 +4,9 @@
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa": { "exe": "test" },
"flexiprep": {
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
"fastqc": {"exe":"test"},
"cutadapt": {"exe":"test"},
"sickle": {"exe":"test"}
},
"chunking": false
}
pipeline-template/examples/test.json
+ 4
− 4
View file @ 8a242160
{
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"gatk": {"flexiprep": { "sdfg": { "exe": "gatk" }}},
"pbzip2": { "exe": "/home/pjvan_thof/pipelines/test/test" },
"pbzip2": { "exe": "test" },
"flexiprep": {
"fastqc": { "exe": "/home/pjvan_thof/pipelines/test/test" },
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
"fastqc": { "exe": "test" },
"cutadapt": {"exe":"test"},
"sickle": {"exe":"test"}
}
}
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