added wget script

broadinstitute · Oct 16, 2024 · 412ea83 · 412ea83
1 parent 277a7a6
commit 412ea83
Showing 1 changed file with 7 additions and 3 deletions.
diff --git a/beta-pipelines/skylab/slidetags/spatial-count/spatial-count.wdl b/beta-pipelines/skylab/slidetags/spatial-count/spatial-count.wdl
@@ -22,7 +22,8 @@ task count {
  gcloud config set storage/thread_count 2
 
  # Download the script -- put this script into a docker
- ### wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/main/spatial-count/spatial-count.jl
+ wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/5c74e9e6148102081827625b9ce91ec2b7ba3541/spatial-count/spatial-count.jl
+ ls 
 
  echo "FASTQs: ~{length(fastq_paths)} paths provided"
  echo "Pucks: ~{length(pucks)} puck(s) provided"
@@ -57,8 +58,11 @@ task count {
 
  # Run the script
  echo ; echo "Running spatial-count.jl"
- julia --threads=4 /spatial-count.jl fastqs pucks .
-
+ ## julia --threads=4 /spatial-count.jl fastqs pucks .
+ julia --threads=4 spatial-count.jl fastqs pucks .
+ echo "TEST"
+ ls
+
  if [[ -f SBcounts.h5 ]] ; then
  echo ; echo "Success, uploading counts"
  echo "true" > DONE