Commit 73091256 authored by Sander Bollen's avatar Sander Bollen
Browse files

remove OUTPUT_DIR config value

parent a62d53f9
......@@ -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 \
......
......@@ -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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