Commit c5677473 authored by van den Berg's avatar van den Berg
Browse files

Reorganise the test data, add readgroups test

parent 6475508a
......@@ -3,13 +3,13 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz"],
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"],
"reference": "/this/file/is/not/there"
}
......@@ -3,12 +3,12 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz"]
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"]
}
......@@ -3,13 +3,13 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"reference":"tests/data/ref.fa",
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz"]
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"]
}
......@@ -3,14 +3,14 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"reference":"tests/data/ref.fa",
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz"],
"bedfile": "tests/data/full_chrM.bed"
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"],
"bedfile": "tests/data/reference/full_chrM.bed"
}
......@@ -3,14 +3,14 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"reference":"tests/data/ref.fa",
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz"],
"refflat": "tests/data/chrM_refFlat.txt"
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"],
"refflat": "tests/data/reference/chrM_refFlat.txt"
}
......@@ -3,14 +3,14 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"reference":"tests/data/ref.fa",
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz"],
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"],
"scatter_size": 1000
}
......@@ -3,13 +3,13 @@
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/micro_R1.fq.gz",
"R2": "tests/data/micro_R2.fq.gz"
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"reference":"tests/data/ref.fa",
"dbsnp": "tests/data/database.vcf.gz",
"known_sites": ["tests/data/database.vcf.gz", "tests/data/database.vcf.gz"]
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz", "tests/data/reference/database.vcf.gz"]
}
{
"samples": {
"micro": {
"libraries": {
"lib_01": {
"R1": "tests/data/fastq/micro_rg1_R1.fq.gz",
"R2": "tests/data/fastq/micro_rg1_R2.fq.gz"
},
"lib_02": {
"R1": "tests/data/fastq/micro_rg2_R1.fq.gz",
"R2": "tests/data/fastq/micro_rg2_R2.fq.gz"
}
}
}
},
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"],
"bedfile": "tests/data/reference/full_chrM.bed"
}
......@@ -9,3 +9,9 @@ fastq.
The `ref.fa` fasta file contains human mitochondrial genome (NC_012920).
The `database.vcf.gz` VCF file contains a single artificial variant.
The `micro_rg1_R1.fq.gz` and `micro_rg1_R2.fq.gz` were created by taking the
first 15440 lines from `micro_R1.fq.gz` and `micro_R2.fq.gz, respectively.
The `micro_rg2_R1.fq.gz` and `micro_rg2_R2.fq.gz` were created by taking the
last 15440 lines from `micro_R1.fq.gz` and `micro_R2.fq.gz, respectively.
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment