diff --git a/.github/workflows/test_run_dataset_R.yml b/.github/workflows/test_run_dataset_R.yml index b86fcd6..37ec7fb 100644 --- a/.github/workflows/test_run_dataset_R.yml +++ b/.github/workflows/test_run_dataset_R.yml @@ -34,9 +34,11 @@ jobs: nextflow self-update - name: Run pipeline with test data + shell: bash run: | nextflow run main.nf -profile test,docker --mode run_dataset \ --methods rctd,music,spatialdwls,nnls,seurat + echo $(ls) - name: Upload proportions and metrics uses: actions/upload-artifact@v3 diff --git a/conf/test.config b/conf/test.config index 64bebda..da16b5b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -31,6 +31,7 @@ params { trace { enabled = true + file = 'trace.txt' fields = 'task_id,hash,name,tag,status,exit,container,duration,realtime,cpus,disk,memory,attempt,%cpu,%mem,rss,peak_rss,vmem,peak_vmem' }