Update wrapper

bgruening · Aug 31, 2023 · fc74906 · fc74906
1 parent 4f0e976
commit fc74906
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
@@ -29,6 +29,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  @PREPROCESSING@
  
  mkdir -p './aligned' &&
+ mkdir -p './kvdb_folder' &&
 
  sortmerna
  #for $i, $reference in enumerate($ref)
@@ -78,14 +79,13 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  --gap_ext '$gap_ext'
  --threads \${GALAXY_SLOTS:-1}
  -m \${GALAXY_MEMORY_MB:-8192}
- --kvdb './'
+ --kvdb 'kvdb_folder'
  #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
  --out2
  #end if
  #if $report.report_type != 'None'
  && samtools view -@ "\${GALAXY_SLOTS:-4}" -u aligned.sam | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o '$output_bam'
  #end if
- && ls -lah
 ]]>
  </command>
  <inputs>