ExomeDepth with nextflow runs with premade references

pipeline/cnv_calling.nf

@@ -143,15 +143,11 @@ process run_exomedepth {
    
    if [ \${sex} == 1 ]; then
        
-   Rscript $workflow.projectDir/pipeline/ExomeDepth_assets/ExomeDepth_basic_own_vignette.R -r $workflow.projectDir/pipeline/ExomeDepth_assets/male_reference_dataframe.csv -i \${bam_path} -o $workflow.projectDir/\${fam_id} -b ${target_bed} -f ${reference_genome} -t \${bam_file}
+       Rscript $workflow.projectDir/pipeline/ExomeDepth_assets/ExomeDepth_basic_own_vignette.R -r $workflow.projectDir/pipeline/ExomeDepth_assets/male_reference_dataframe.csv -i \${bam_path} -o $workflow.projectDir/\${fam_id} -b ${target_bed} -f ${reference_genome} -t \${bam_file}
 
-   elif [ \${sex} == 2 ]; then
+   else [ \${sex} == 2 ]
 
-   Rscript $workflow.projectDir/pipeline/ExomeDepth_assets/ExomeDepth_basic_own_vignette.R -r $workflow.projectDir/pipeline/ExomeDepth_assets/male_reference_dataframe.csv -i \${bam_path} -o  $workflow.projectDir/\${fam_id} -b ${target_bed} -f ${reference_genome} -t \${bam_file}
-
-   else
-
-       # to do
+       Rscript $workflow.projectDir/pipeline/ExomeDepth_assets/ExomeDepth_basic_own_vignette.R -r $workflow.projectDir/pipeline/ExomeDepth_assets/male_reference_dataframe.csv -i \${bam_path} -o  $workflow.projectDir/\${fam_id} -b ${target_bed} -f ${reference_genome} -t \${bam_file}
 
    fi