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Klinische Genetica
capture-lumc
hutspot
Commits
73091256
Commit
73091256
authored
Mar 21, 2019
by
Sander Bollen
Browse files
remove OUTPUT_DIR config value
parent
a62d53f9
Changes
2
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README.md
View file @
73091256
...
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@@ -113,7 +113,6 @@ The following configuration values are **required**:
| configuration | description |
| ------------- | ----------- |
|
`OUTPUT_DIR`
| Absolute path to output directory |
|
`REFERENCE`
| Absolute path to fasta file |
|
`SAMPLE_CONFIG`
| Path to config file as described above |
|
`GATK`
| Path to GATK jar.
**Must**
be version 3.7 |
...
...
@@ -169,7 +168,6 @@ snakemake -s Snakefile \
--restart-times
2
\
-T
\
--config
SAMPLE_CONFIG
=
samples.json
\
OUTPUT_DIR
=
/path/to/odir
\
REFERENCE
=
/path/to/genome.fasta
\
GATK
=
/path/to/GenomeAnalysisTK.jar
\
DBSNP
=
/path/to/dbsnp.vcf.gz
\
...
...
Snakefile
View file @
73091256
...
...
@@ -28,10 +28,6 @@ from pathlib import Path
from pyfaidx import Fasta
OUT_DIR = config.get("OUTPUT_DIR") # TODO: use regular snakemake option?
if OUT_DIR is None:
raise ValueError("You must set --config OUT_DIR=<path>")
REFERENCE = config.get("REFERENCE")
if REFERENCE is None:
raise ValueError("You must set --config REFERENCE=<path>")
...
...
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