Fixed log definition in wrappers.

bihealth · Jun 28, 2022 · be05d60 · be05d60
1 parent 59315cd
commit be05d60
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/snappy_wrappers/wrappers/mutect2/contamination/wrapper.py b/snappy_wrappers/wrappers/mutect2/contamination/wrapper.py
@@ -18,13 +18,13 @@
 export LD_LIBRARY_PATH=$(dirname $(which bgzip))/../lib
 
 # Also pipe everything to log file
-if [[ -n "{snakemake.log}" ]]; then
+if [[ -n "{snakemake.log.log}" ]]; then
     if [[ "$(set +e; tty; set -e)" != "" ]]; then
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        exec &> >(tee -a "{snakemake.log}" >&2)
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        exec &> >(tee -a "{snakemake.log.log}" >&2)
     else
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        echo "No tty, logging disabled" >"{snakemake.log}"
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        echo "No tty, logging disabled" >"{snakemake.log.log}"
     fi
 fi
 

diff --git a/snappy_wrappers/wrappers/mutect2/filter/wrapper.py b/snappy_wrappers/wrappers/mutect2/filter/wrapper.py
@@ -18,13 +18,13 @@
 export LD_LIBRARY_PATH=$(dirname $(which bgzip))/../lib
 
 # Also pipe everything to log file
-if [[ -n "{snakemake.log}" ]]; then
+if [[ -n "{snakemake.log.log}" ]]; then
     if [[ "$(set +e; tty; set -e)" != "" ]]; then
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        exec &> >(tee -a "{snakemake.log}" >&2)
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        exec &> >(tee -a "{snakemake.log.log}" >&2)
     else
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        echo "No tty, logging disabled" >"{snakemake.log}"
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        echo "No tty, logging disabled" >"{snakemake.log.log}"
     fi
 fi