add special case for BAM files

2026-10-24 02:04:04 +08:00 · 2025-09-25 16:05:34 +02:00
parent 3481880c41
commit 117a793412
1 changed files with 3 additions and 0 deletions
@@ -55,6 +55,9 @@
                #set $cleaned_name = str($count + 1) + '_' + re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
                echo "[`date`] - Linking '$file' to '/home/rstudio/galaxy_inputs/${cleaned_name}.${file.ext}'" &&
                ln -sf '$file' '/home/rstudio/galaxy_inputs/${cleaned_name}.${file.ext}' &&
+                #if $file.ext == 'bam':
+                    ln -s '$file.metadata.bam_index' '/home/rstudio/galaxy_inputs/${cleaned_name}.bam.bai' &&
+                #end if
            #end for
        #else
            echo "[`date`] - No input files provided, skipping file linking step." &&