From 550500418509073fbbb13dac98a2522b767819e9 Mon Sep 17 00:00:00 2001
From: npetrill <npetrill@broadinstitute.org>
Date: Thu, 14 Nov 2024 09:17:14 -0500
Subject: [PATCH] cleaning up

---
 tasks/skylab/StarAlign.wdl | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index 0a33290dd8..e6bab0a74a 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -333,17 +333,6 @@ task STARsoloFastq {
     # validate the bam with samtools quickcheck
     samtools quickcheck -v Aligned.sortedByCoord.out.bam
 
-    samtools quickcheck *.bam && echo 'all ok' \
-    || echo 'fail!'
-
-    # wait until star completes, then write out complete.txt file
-    wait
-
-    touch STARsolo_completed.txt
-    echo "done" > STARsolo_completed.txt
-
-    echo "STARsolo command completed with exit code $?"
-
 
     echo "UMI LEN " $UMILen