extract ids, sex and path from ped and samplesheet in cnv-calling

pipeline/cnv_calling.nf

@@ -104,15 +104,20 @@ process run_exomedepth {
    input:
    path(target_bed)
    path(reference_genome) 
-   tuple val(ped_file_info)
-   tuple val(samplesheet_info)
-   
-   script:
+   val(ped_file_info)
+   val(samplesheet_info)
 
+   script:
+            
    """
-   ind_id=\$(${ped_file_info}[0])
-   fam_id=\$(${ped_file_info}[1])
-   sex=\$(${ped_file_info}[4])
+   ind_id=\$(echo ${ped_file_info} |cut -c2- | cut -d',' -f1)
+   fam_id=\$(echo ${ped_file_info} |cut -c2- | cut -d',' -f2)
+   sex=\$(echo ${ped_file_info} |cut -c2- | cut -d',' -f5)
+   
+   # echo ${ped_file_info}
+   # echo ${samplesheet_info}
+   
+   bam_path=\$(echo ${samplesheet_info} | cut -d',' -f4 | cut -c3- | rev | cut -c3- | rev)
    
    # bam_path 
    # take the pedfile info of a sample, if sex = 1 use male reference if sex = 2 use female reference 
@@ -123,7 +128,8 @@ process run_exomedepth {
    echo \${ind_id}
    echo \${fam_id}
    echo \${sex}
-   echo ${samplesheet_info}
+   echo \${bam_path}
+   
    # Rscript $workflow.projectDir/pipeline/ExomeDepth_assets/ExomeDepth_basic_own_vignette.R -i $workflow.projectDir/pipeline/ExomeDepth_assets/HG003_4_paths.txt -b ${target_bed} -f ${reference_genome} -t HG002.recal.bam -o $workflow.projectDir/pipeline/ExomeDepth_assets
    """