samtools version and dorado outputs

theiagen · Nov 15, 2024 · 1bc7bb0 · 1bc7bb0
1 parent 5d3b91f
commit 1bc7bb0
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/tasks/basecalling/task_dorado_demux.wdl b/tasks/basecalling/task_dorado_demux.wdl
@@ -16,7 +16,7 @@ task dorado_demux {
     set -euo pipefail
 
     # Capture Dorado version
-    dorado --version | tee DORADO_VERSION
+    dorado --version 2>&1 | tee DORADO_VERSION
     echo "Dorado version:" $(cat DORADO_VERSION)
 
     # Output the Dorado model used

diff --git a/tasks/basecalling/task_samtools_convert.wdl b/tasks/basecalling/task_samtools_convert.wdl
@@ -13,7 +13,7 @@ task samtools_convert {
     set -euo pipefail
 
     # samtools version
-    samtools --version | tee SAMTOOLS_VERSION
+    samtools --version | head -n1 | tee VERSION
 
     bam_output="output/bam/"
     mkdir -p "$bam_output"