WIP: testing. uncomment CI for scRNA

maxplanck-ie · Aug 13, 2024 · 882d28e · 882d28e
1 parent ca94ebd
commit 882d28e
Showing 1 changed file with 2 additions and 6 deletions.
diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -372,12 +372,8 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1338 ]; then exit 1 ; fi
 #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1038 ]; then exit 1 ; fi
 #WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
 #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1015 ]; then exit 1 ; fi
-echo "===scRNAseq testing: start==="
-scr_out=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml`
-echo $scr_out
-echo "===scRNAseq testing: end==="
-WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1642 ]; then exit 1 ; fi
+#WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
+#if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1642 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1485 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`