WIP: CI testing

maxplanck-ie · Aug 12, 2024 · 2ff76da · 2ff76da
1 parent a62299f
commit 2ff76da
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -372,6 +372,10 @@ 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 ] || [ $WC -ne 1642 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`

diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -42,7 +42,6 @@ jobs:
         ruff check .
   CI:
     runs-on: ubuntu-latest
-    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v3