From 7a1f120fe02cc427b73a0ceeaf9aa3907edf1343 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Tue, 30 Apr 2019 11:57:37 +0200
Subject: [PATCH] -T no longer exists in snakemake 5

---
 README.md                      | 2 --
 tests/test_functional_run.yml  | 2 +-
 tests/test_integration_run.yml | 4 ++--
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index f771362..56eca2f 100644
--- 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
index ba5b9aa..13e6984 100644
--- 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
index 6964e30..3a12b67 100644
--- 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