Commit 7a1f120f authored by Sander Bollen's avatar Sander Bollen
Browse files

-T no longer exists in snakemake 5

parent 2b1f5ca3
Pipeline #2551 passed with stages
in 21 minutes and 26 seconds
......@@ -99,7 +99,6 @@ the pipeline can be started with:
```bash
snakemake -s Snakefile \
--use-conda \
-T \
--config <CONFIGURATION VALUES>
```
......@@ -166,7 +165,6 @@ snakemake -s Snakefile \
-w 120 \
--max-jobs-per-second 30 \
--restart-times 2 \
-T \
--config SAMPLE_CONFIG=samples.json \
REFERENCE=/path/to/genome.fasta \
GATK=/path/to/GenomeAnalysisTK.jar \
......
......@@ -4,7 +4,7 @@
snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
--cluster "sbatch --parsable"
--cluster-status "${PWD}/cluster/slurm-cluster-status/slurm-cluster-status.py"
-r -p -s Snakefile -T
-r -p -s Snakefile
--config JAVA=$(which java)
REFERENCE=${FUNCTIONAL_REF} GATK=${GATK_JAR}
DBSNP=${FUNCTIONAL_DBSNP}
......
- name: test-functional-run
- name: test-integration-run
command: >-
bash -c '
snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
--cluster "sbatch --parsable" -r -p -s Snakefile -T
--cluster "sbatch --parsable" -r -p -s Snakefile
--config JAVA=$(which java)
REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
DBSNP=tests/data/database.vcf.gz
......
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