run_exomedepth works, adding process to get proband cnvs that are not in parents

pipeline/cnv_calling.nf

@@ -91,34 +91,37 @@ process check_ped_file {
    cat $ped_file
    """
 }
-
-// process to split ped files into families - send each family to extract_target
-// this is done by inputs  
-
-// extract_target: take a family and identify the sex. use the sample sheet to get the path to the bam file 
-// emit a paired object, indicating the sex and the path to the bam file  
   
 process run_exomedepth {
    label 'medium'
 
+   // Take the ped_file line and sample sheet line of a sample, collect relevant information and run exomedepth
+   // This assumes that the information coming from the input sample channel are in the same order 
+   // so information recieved is for the same sample 
+
+   // Want to emit a channel of family IDs for next process to use so can find relevant files 
+
    input:
    path(target_bed)
    path(reference_genome) 
    val(ped_file_info)
    val(samplesheet_info)
 
+   output:
+   val \${fam_id} into family_ids
+
    script:
             
    """
    ind_id=\$(echo ${ped_file_info} |cut -c2- | cut -d',' -f1)
-   fam_id=\$(echo ${ped_file_info} |cut -c2- | cut -d',' -f2)
+   fam_id=\$(echo ${ped_file_info} |cut -c2- | cut -d',' -f2 | cut -c2-)
    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 
    # create an input file, adding the path to target to the reference, using cat [bam path from sample_sheet_info] and reference file 
@@ -129,16 +132,52 @@ process run_exomedepth {
    echo \${fam_id}
    echo \${sex}
    echo \${bam_path}
+
+   bam_file=\$(echo \${bam_path} | awk -F"/" '{print \$NF}')
    
-   # 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 $workflow.projectDir/pipeline/ExomeDepth_assets
+   # if directory for family doesnt exist, create it 
+   mkdir -p  "$workflow.projectDir/\${fam_id}"
+
+   # make reference file for sample, store in fam directory, depending on sex, if sex is not known use both, maybe return a warning
+   
+   if [ \${sex} == 1 ]; then
+       
+       cp  $workflow.projectDir/pipeline/ExomeDepth_assets/mini_male_reference.txt $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+       echo \${bam_path} >> $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+
+   elif [ \${sex} == 2 ]; then
+
+       cp  $workflow.projectDir/pipeline/ExomeDepth_assets/mini_female_reference.txt $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+       echo \${bam_path} >> $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+
+   else
+
+       cp  $workflow.projectDir/pipeline/ExomeDepth_assets/mini_male_reference.txt $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+       cat  $workflow.projectDir/pipeline/ExomeDepth_assets/mini_female_reference.txt >> $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+       echo \${bam_path} >> $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt
+
+   fi
+
+   # Rscript $workflow.projectDir/pipeline/ExomeDepth_assets/ExomeDepth_basic_own_vignette.R -i $workflow.projectDir/\${fam_id}/\${ind_id}_bam_paths.txt -b ${target_bed} -f ${reference_genome} -t \${bam_file} -o $workflow.projectDir/\${fam_id}
    """
 
 }
 
-// future process to reformat output
-
 // future process to compare proband to parents 
 
+process collect_proband_cnvs {
+
+   input:
+   val(family_ids)
+
+   script:
+   
+   """
+   echo $family_ids
+   """
+
+}
+
 // future process for gnomAD
 
 workflow check_inputs {
@@ -147,4 +186,6 @@ workflow check_inputs {
     check_sample_sheet(read_inputs.out.ch_samplesheet)
     check_ped_file(read_inputs.out.ch_ped_file)
     run_exomedepth(params.target_bed, params.reference_genome, read_inputs.out.ch_ped_file_info, read_inputs.out.ch_samplesheet_info)
+    collect_proband_cnvs(run_exomedepth.out.ch_family_ids)
+
 }