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Klinische Genetica
capture-lumc
hutspot
Commits
c5677473
Commit
c5677473
authored
Apr 17, 2020
by
van den Berg
Browse files
Reorganise the test data, add readgroups test
parent
6475508a
Changes
28
Hide whitespace changes
Inline
Side-by-side
tests/data/config/invalid_config_fake_ref.json
View file @
c5677473
...
...
@@ -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"
}
tests/data/config/invalid_config_no_ref.json
View file @
c5677473
...
...
@@ -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"
]
}
tests/data/config/sample_config.json
View file @
c5677473
...
...
@@ -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"
]
}
tests/data/config/sample_config_bed_all.json
View file @
c5677473
...
...
@@ -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"
}
tests/data/config/sample_config_refflat.json
View file @
c5677473
...
...
@@ -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"
}
tests/data/config/sample_config_scatter.json
View file @
c5677473
...
...
@@ -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
}
tests/data/config/sample_config_two_known_vcf.json
View file @
c5677473
...
...
@@ -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"
]
}
tests/data/config/sample_config_two_readgroup.json
0 → 100644
View file @
c5677473
{
"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"
}
tests/data/README.md
→
tests/data/
fastq/
README.md
View file @
c5677473
...
...
@@ -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.
tests/data/micro_R1.fq.gz
→
tests/data/
fastq/
micro_R1.fq.gz
View file @
c5677473
File moved
tests/data/micro_R2.fq.gz
→
tests/data/
fastq/
micro_R2.fq.gz
View file @
c5677473
File moved
tests/data/fastq/micro_rg1_R1.fq.gz
0 → 100644
View file @
c5677473
File added
tests/data/fastq/micro_rg1_R2.fq.gz
0 → 100644
View file @
c5677473
File added
tests/data/fastq/micro_rg2_R1.fq.gz
0 → 100644
View file @
c5677473
File added
tests/data/fastq/micro_rg2_R2.fq.gz
0 → 100644
View file @
c5677473
File added
tests/data/chrM_refFlat.txt
→
tests/data/
reference/
chrM_refFlat.txt
View file @
c5677473
File moved
tests/data/database.vcf.gz
→
tests/data/
reference/
database.vcf.gz
View file @
c5677473
File moved
tests/data/database.vcf.gz.tbi
→
tests/data/
reference/
database.vcf.gz.tbi
View file @
c5677473
File moved
tests/data/full_chrM.bed
→
tests/data/
reference/
full_chrM.bed
View file @
c5677473
File moved
tests/data/ref.dict
→
tests/data/
reference/
ref.dict
View file @
c5677473
File moved
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