Merge pull request #649 from wtsi-npg/devel

merge from devel to master to create release 67.3.0
wtsi-npg · Oct 10, 2019 · 43d6a7f · 43d6a7f
2 parents 9511d20 + 0badd9d
commit 43d6a7f
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Showing 3 changed files with 32 additions and 3 deletions.
diff --git a/Changes b/Changes
@@ -1,5 +1,11 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+release 67.3.0
+  - change default file type to cram for genotype check
+  - script for skippimg manual QC step: an additional filter
+    to ensure that the all lanes for a run that bypasses
+    manual QC deplexed properly
+
 release 67.2.0
   - script to move NovaSeq runs for a particular study
   - change default file type to cram for bam_flagstats

diff --git a/bin/npg_mqc_skipper b/bin/npg_mqc_skipper
@@ -22,6 +22,7 @@ Readonly::Scalar my $NUM_DISTINCT_STUDIES => 1;
 Readonly::Scalar my $RUN_STATUS_FROM      => 'qc review pending';
 Readonly::Scalar my $RUN_STATUS_TO        => 'archival pending';
 Readonly::Scalar my $INSTRUMENT_MODEL     => 'NovaSeq';
+Readonly::Scalar my $DEPLEXING_PERCENT_THRESHOLD => 93;
 
 my $dry_run = 1;
 my $study_name;
@@ -57,8 +58,13 @@ if (!@rows) {
   exit 0;
 }
 
+my $run_list = sub {
+  my @ids = @_;
+  return join q[,], map { q[?] } @ids;
+};
+
 my @run_ids = map { $_->id_run } @rows;
-my $placeholders = join q[,], map { q[?] } @run_ids;
+my $placeholders = $run_list->(@run_ids);
 
 my $dbh = WTSI::DNAP::Warehouse::Schema->connect->storage->dbh;
 my $query =
@@ -78,6 +84,22 @@ while (my @data = $sth->fetchrow_array()) {
    push @run_ids, $data[0];
 }
 
+if (@run_ids) {
+  $placeholders = $run_list->(@run_ids);
+  $query =  q[select distinct(id_run) from iseq_run_lane_metrics ] .
+            q[where (tags_decode_percent is null or tags_decode_percent < ?) ] .
+           qq[and id_run in (${placeholders})];
+  $sth = $dbh->prepare($query) or croak "Failed to prepare statement: $DBI::errstr";
+  $sth->execute($DEPLEXING_PERCENT_THRESHOLD, @run_ids);
+  my $temp = {};
+  while (my @data = $sth->fetchrow_array()) {
+     $temp->{$data[0]} = 1;
+  }
+  if (keys %{$temp}) {
+    @run_ids = grep { not $temp->{$_} } @run_ids;
+  }
+}
+
 if (@run_ids) {
   $logger->info(join qq[\n\t], q[],
                 qq[Study '$study_name'],
@@ -179,7 +201,8 @@ npg_mqc_skipper --study_name 'SOME STUDY' --no-dry_run
 
 In dry run mode this script identifies and reports runs having
 'qc review pending' status where all samples apart from controls
-belong to the study given as the --study_name argument.
+belong to the study given as the --study_name argument and
+deplexing percent for all lanes of any such run is 93% or above.
 
 In non-dry run mode the status of this runs is changed to
 'archival pending', ie the manual QC stage of the run life cycle

diff --git a/lib/npg_qc/autoqc/checks/genotype.pm b/lib/npg_qc/autoqc/checks/genotype.pm
@@ -29,7 +29,7 @@ Readonly::Scalar my $SAMTOOLS_EXTRACT_REGIONS_NAME => q[samtools];
 Readonly::Scalar my $SAMTOOLS_MERGE_NAME => q[samtools];
 Readonly::Scalar my $SAMTOOLS_MPILEUP_NAME => q[samtools];
 Readonly::Scalar my $BCFTOOLS_NAME => q[bcftools];
-Readonly::Scalar our $EXT => q[bam];
+Readonly::Scalar our $EXT => q[cram];
 Readonly::Scalar my $SEQUENOM_QC_PLEX => q[W30467];
 Readonly::Scalar my $DEFAULT_QC_PLEX => q[sequenom_fluidigm_combo];
 Readonly::Scalar my $DEFAULT_SNP_CALL_SET => q[W30467];