fix: gcnv wrapper regex curly-brackets parsed by python string format…

…ting (#489 ) (#501)
bihealth · Apr 15, 2024 · 8fb40e5 · 8fb40e5
1 parent 6993233
commit 8fb40e5
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py b/snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py
@@ -44,7 +44,7 @@
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
 
 # Get contig name style
-egrep "^@SQ\s+SN:chr[0-9XY]{1,2}\s+" {snakemake.input.interval_list} > /dev/null && true
+egrep "^@SQ\s+SN:chr[0-9XY]{{1,2}}\s+" {snakemake.input.interval_list} > /dev/null && true
 exit_status=$?
 if [[ $exit_status == 0 ]]; then
     STYLE="chr"

diff --git a/snappy_wrappers/wrappers/gcnv/post_germline_calls/wrapper.py b/snappy_wrappers/wrappers/gcnv/post_germline_calls/wrapper.py
@@ -28,7 +28,7 @@
 # Get contig name style
 # Note: the sample_index in '{snakemake.input.ploidy}' and '{snakemake.input.calls[0]}' are NOT guaranteed to be the same
 # -> Sample_0 should always exist and the contig names (which we care for) are the same
-tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | egrep "^chr[0-9XY]{1,2}\s[0-9]\s[0-9.]+" > /dev/null && true
+tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | egrep "^chr[0-9XY]{{1,2}}\s[0-9]\s[0-9.]+" > /dev/null && true
 exit_status=$?
 if [[ $exit_status == 0 ]]; then
     STYLE="chr"

diff --git a/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py b/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py
@@ -30,7 +30,7 @@
 fi
 
 # Get contig name style; SAMPLE_0  is guaranteed to exist
-tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | grep "^chr[0-9XY]{1,2}\s[0-9]\s[0-9.]+$" > /dev/null && true
+tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | grep "^chr[0-9XY]{{1,2}}\s[0-9]\s[0-9.]+$" > /dev/null && true
 exit_status=$?
 if [[ $exit_status == 0 ]]; then
     STYLE="chr"