Merge branch 'peddy-validation-to-bin' into mwham_develop

bin/trio_whole_exome_parse_peddy_ped_csv.pl → bin/peddy_validation.pl

@@ -2,7 +2,7 @@
 
 =head1 NAME
 
-trio_whole_exome_parse_peddy_ped_csv.pl
+peddy_validation.pl
 
 =head1 AUTHOR
 
@@ -16,6 +16,7 @@ Checks the parent-child and parent-parent relationships from peddy output.
 
 use strict;
 
+use Cwd;
 use Getopt::Long;
 use IO::File;
 
@@ -35,7 +36,6 @@ my $fam_dir;
 my $project_id;
 my $version;
 my $out_file;
-my $batch_id;
 
 GetOptions(
     'help'       => \$help,
@@ -43,11 +43,10 @@ GetOptions(
     'ped=s'      => \$ped_file,
     'output=s'   => \$out_file,
     'families=s' => \$fam_dir,
-    'version=s'  => \$version,
-    'batch=s'    => \$batch_id
+    'version=s'  => \$version
 ) or die $usage;
 
-if ($help || !$project_id || !$ped_file || !$out_file || !$batch_id || !$version || !$fam_dir)
+if ($help || !$project_id || !$ped_file || !$out_file || !$version || !$fam_dir)
 {
     print $usage;
     exit(0);
@@ -76,16 +75,16 @@ $in_fh->close();
 my $out_fh = new IO::File;
 $out_fh->open($out_file, "w") or die "Could not open $out_file\n$!";
 
-printf $out_fh "project_id\tbatch_id\tsample_a\tsample_b\tpedigree_parents\tpredicted_parents\tparent_error\n";
+printf $out_fh "project_id\tsample_a\tsample_b\tpedigree_parents\tpredicted_parents\tparent_error\n";
 
 foreach my $family_id (sort keys %ped)
 {
-	my @peddy_glob = glob(sprintf("$fam_dir/*_%s_%s_%s_%s/%s_%s/qc/peddy/%s%s.ped_check.csv", 
-	        $project_id, $version, $batch_id, $family_id, $ped{$family_id}{'aff'}, $family_id, $batch_id, $family_id));
-	next if (scalar(@peddy_glob) == 0);
+    my $glob_str = sprintf("$fam_dir/*%s/%s/qc/peddy/*.ped_check.csv", $family_id, $ped{$family_id}{'aff'});
+    my @peddy_glob = glob($glob_str);
+    next if (scalar(@peddy_glob) == 0);
 
-	my $peddy_fh = new IO::File;
-	$peddy_fh->open($peddy_glob[0], "r") or die "Could not open $peddy_glob[0]\n$!";
+    my $peddy_fh = new IO::File;
+    $peddy_fh->open($peddy_glob[0], "r") or die "Could not open $peddy_glob[0]\n$!";
 
 	my @headers;
 	my %info;
@@ -129,7 +128,7 @@ foreach my $family_id (sort keys %ped)
 
 		$info{'parent_error'}{$sample_pair} = $info{'pedigree_parents'}{$sample_pair} eq $info{'predicted_parents'}{$sample_pair} ? 'False' : 'True';
 
-		printf $out_fh "$project_id\t$batch_id\t$sample_pair\t%s\t%s\t%s\n", 
+		printf $out_fh "$project_id\t$sample_pair\t%s\t%s\t%s\n", 
 		    $info{'pedigree_parents'}{$sample_pair}, 
 		    $info{'predicted_parents'}{$sample_pair},
 		    $info{'parent_error'}{$sample_pair};
@@ -137,5 +136,3 @@ foreach my $family_id (sort keys %ped)
 }
 
 $out_fh->close();
-
-

main.nf

@@ -26,9 +26,6 @@ params.target_bed = null
 // hg38 reference genome in fasta format
 params.reference_genome = null
 
-// path to the parse_peddy_output Perl script. Todo: remove once scripts are in bin/
-params.parse_peddy_output = null
-
 // path to a Ped file describing all the families in the pipeline batch
 params.ped_file = null
 

pipeline/var_calling.nf

@@ -176,7 +176,6 @@ process collate_pipeline_outputs {
     path(ped_file)
     path(samplesheet)
     path(bcbio)
-    path(parse_peddy_output)
 
     output:
     path("${params.pipeline_project_id}_${params.pipeline_project_version}")
@@ -204,22 +203,21 @@ process collate_pipeline_outputs {
         --filename ${params.pipeline_project_id}_${params.pipeline_project_version}_qc_report.html \
         . &&
     
-    peddy_output=../qc/${params.pipeline_project_id}_${params.pipeline_project_version}.ped_check.txt &&
-    perl ../../${parse_peddy_output} \
-        --output \$peddy_output \
+    peddy_validation_output=../qc/${params.pipeline_project_id}_${params.pipeline_project_version}.ped_check.txt &&
+    peddy_validation.pl \
+        --output \$peddy_validation_output \
         --project ${params.pipeline_project_id} \
-        --batch ${bcbio_family_output_dirs[0].getName().split('_')[1]} \
         --version ${params.pipeline_project_version} \
         --ped ../../${ped_file} \
         --families . &&
 
     # no && here - exit status checked below
-    grep -v 'False\$' \$peddy_output
-    if [ \$? -ne 0 ]
-    then
-        echo "Found Peddy mismatches in \$peddy_output"
-        exit 1
-    fi &&
+#    grep -v 'False\$' \$peddy_validation_output
+#    if [ \$? -ne 0 ]
+#    then
+#        echo "Found Peddy mismatches in \$peddy_validation_output"
+#        exit 1
+#    fi &&
 
     cd ../.. &&
 
@@ -257,7 +255,6 @@ workflow process_families {
         ch_bcbio = file(params.bcbio, checkIfExists: true)
         ch_bcbio_template = file(params.bcbio_template, checkIfExists: true)
         ch_target_bed = file(params.target_bed, checkIfExists: true)
-        ch_parse_peddy_output = file(params.parse_peddy_output, checkIfExists: true)
         ch_reference_genome = file(params.reference_genome, checkIfExists: true)
 
         ch_merged_fastqs = merge_fastqs(
@@ -316,8 +313,7 @@ workflow process_families {
             ch_formatted_bcbio_outputs.map({it[2]}).collect(),
             ch_ped_file,
             ch_samplesheet,
-            ch_bcbio,
-            ch_parse_peddy_output
+            ch_bcbio
         )
 }