concoct: use bai from metadata

Author: bernt-matthias

tools/concoct/concoct_coverage_table.xml

@@ -10,15 +10,13 @@
 mkdir 'mapping' &&
 #if $mode.type == 'individual'
     #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.bamfile))
-ln -s '$mode.bamfile' 'mapping/${identifier}.sorted.bam' &&
-samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
-mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
+    ln -s '$mode.bamfile' 'mapping/${identifier}.bam' &&
+    ln -s '$mode.bamfile.metadata.bam_index' 'mapping/${identifier}.bam.bai'
 #else
     #for $e in $mode.bamfiles
         #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
-ln -s '$e' 'mapping/${identifier}.sorted.bam' &&
-samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
-mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
+        ln -s '$e' 'mapping/${identifier}.bam' &&
+        ln -s '$e.metadata.bam_index' 'mapping/${identifier}.bam.bai' &&
     #end for
 #end if
 concoct_coverage_table.py