#for $alignment in $alignments
            ln -f -s '${alignment.metadata.bam_index}' '${alignment}.bai' &&
        #end for
        
        sambamba mpileup
            -t \${GALAXY_SLOTS:-4}
            
            #for $alignment in $alignments
                 '${alignment}'
            #end for
            
            --samtools
                -f
                #if $reference_genome_source.source_select == "indexed_filtered"
                    '$reference_genome_source.reference_genome'
                #else if $reference_genome_source.source_select == "indexed_all"
                    '$reference_genome_source.reference_genome'
                #else if $reference_genome_source.source_select == "history"
                    '$reference_genome_source.reference_genome'
                #else
                    <!--
                        This is a workaround to obtain the "genome.fa" file that
                        corresponds to the dbkey of the alignments.
                        Because this file is "calculated" during run-time, it can
                        be used in a workflow.
                    -->
                    "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
                #end if

                #if $extended_parameters_regions.sambamba_regions == "region"
                     -r '${extended_parameters_regions.sambamba_r}'
                #elif $extended_parameters_regions.sambamba_regions == "regions_file_pos" or $extended_parameters_regions.sambamba_regions == "regions_file_bed"
                     -l '${extended_parameters_regions.sambamba_l}'
                #end if

                #if $extended_parameters.parameters == "extended"
                    $extended_parameters.sambamba_6
                    $extended_parameters.sambamba_A
                    $extended_parameters.sambamba_B
                     -C $extended_parameters.sambamba_C
                     -d $extended_parameters.sambamba_d
                    $extended_parameters.sambamba_E
                     -M $extended_parameters.sambamba_M
                    $extended_parameters.sambamba_R
                     -q $extended_parameters.sambamba_q
                     -Q $extended_parameters.sambamba_Q

                     -e $extended_parameters.sambamba_e
                     -F $extended_parameters.sambamba_F
                     -h $extended_parameters.sambamba_h
                    $extended_parameters.sambamba_I
                     -L $extended_parameters.sambamba_L
                     -m $extended_parameters.sambamba_m
                     -o $extended_parameters.sambamba_o
                    $extended_parameters.sambamba_p
                     -P $extended_parameters.sambamba_P
                #end if
            | varscan mpileup2snp
             
                #if $extended_parameters.parameters == "extended"
                     --min-coverage     $extended_parameters.varscan_min_coverage
                     --min-reads2       $extended_parameters.varscan_min_reads2
                     --min-avg-qual     $extended_parameters.varscan_min_avg_qual
                     --min-var-freq     $extended_parameters.varscan_min_var_freq
                     --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
                     --p-value          $extended_parameters.varscan_p_value
                                        $extended_parameters.varscan_strand_filter 
                                        $extended_parameters.varscan_variants 
                #end if
            
                #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
                    --output-vcf 1 
                #end if
            
                > '$snv_output'