Move CxG output to root dir for vizapp

vizapp/run_container.sh

@@ -17,7 +17,7 @@ REPO="cellxgene_vip"
 TAG="3.1-small"
 singularity_image=${REPO}-${TAG}.img
 
-outputDir=${outputDir:-"${DIR}/../workflow/output/CELLxGENE/"}
+outputDir=${outputDir:-"${DIR}/../workflow/output/"}
 
 # Run container
 module load singularity/3.9.9

workflow/main.nf

@@ -153,7 +153,7 @@ process quality_control {
 
 //Prepare cellxgene-VIP
 process cxg_setup {
-    publishDir "${projectDir}/output/CELLxGENE", mode: 'copy'
+    publishDir "${projectDir}/output", mode: 'copy'
     container 'git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene/h5ad_convert:0.0.1'
 
     input: