Retrying -r on pod5 convert fast5

aryeelab · Aug 8, 2023 · 9d8c335 · 9d8c335
1 parent af9bd26
commit 9d8c335
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/dorado_basecall.wdl b/dorado_basecall.wdl
@@ -53,15 +53,15 @@ task basecall  {
           mkdir fast5s
           tar zxvf ~{fast5_archive} -C fast5s
           # Convert FAST5 into POD5
-          pod5 convert fast5 ./fast5s/*.fast5 -o pod5s/reads.pod5 --threads 12 
+          pod5 convert fast5 -r fast5s -o pod5s/reads.pod5 --threads 12 
         fi
 
         if [[ "$filetype" == *"Zip archive data"* ]]; then
           echo "FAST5s appear to be compressed with zip. Decompressing..."
           mkdir fast5s 
           unzip ~{fast5_archive} -d fast5s
           # Convert FAST5 into POD5
-          pod5 convert fast5 ./fast5s/*.fast5 -o /pod5s/reads.pod5 --threads 12 
+          pod5 convert fast5 -r fast5s -o pod5s/reads.pod5 --threads 12 
         fi
 
         # Simplex call with --emit-moves and --modified-bases