-T no longer exists in snakemake 5

LUMC · Apr 30, 2019 · 7a1f120 · 7a1f120
1 parent 2b1f5ca
commit 7a1f120
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -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 \

diff --git a/tests/test_functional_run.yml b/tests/test_functional_run.yml
@@ -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}

diff --git a/tests/test_integration_run.yml b/tests/test_integration_run.yml
@@ -1,8 +1,8 @@
-- 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