diff --git a/doc/CHANGELOG.md b/doc/CHANGELOG.md
index 222816cdc..ed46cd2a3 100644
--- a/doc/CHANGELOG.md
+++ b/doc/CHANGELOG.md
@@ -4,6 +4,18 @@ Change log for WTSI genotyping pipeline
 
 Latest version is hosted at: https://github.com/wtsi-npg/genotyping
 
+Release 1.14.1: 2017-03-28
+--------------------------
+
+Added:
+- Fluidigm QC:
+  - Compute QC metrics and write in CSV format
+  - Can update an existing CSV file
+  - Command-line script qc_fluidigm.pl
+- Fluidigm archiver:
+  - Compress Fluidigm data into .tar.gz archive files
+  - Script archive_fluidigm_genotypes.pl
+
 Release 1.14.0: 2017-02-07
 --------------------------
 
@@ -70,76 +82,6 @@ Fixed:
 - Support repeat scans from Infinium database
 
 
-Release 1.13.2: 2016-11-10
---------------------------
-
-Changed:
-- Hotfix: Add cgp and ddd references to WTSI::NPG::Genotyping::QC::Identity
-
-
-Release 1.13.1: 2016-07-28
---------------------------
-
-Changed:
-- Made install.sh more transparent and portable.
-- Updated WTSI-DNAP-Utilities and perl-irods-wrap versions in install.sh.
-
-Fixed:
-- Default LSF queue for Ruby workflows
-
-
-Release 1.13.0: 2016-06-20
---------------------------
-
-Added:
-- install.sh script to install pipeline and its Perl dependencies
-- Documentation for Bayesian identity check
-
-Changed:
-- Modified ready_workflow.pl to better align with user SOP
-- Use try/catch to handle unexpected errors in retrieving QC plex results
-from iRODS
-- Updated reference genome for Sequenom iRODS query
-- Update perl-irods-wrap dependency to 2.4.0; removes unhelpful warning
-messages to STDERR. This in turn requires baton version >= 0.16.4.
-
-Removed:
-- Script publish_infinium_file_list.pl; superseded by other publish scripts
-
-
-Release 1.12.1: 2016-05-13
---------------------------
-
-Fixed:
-- Support repeat scans from Infinium database
-
-
-Release 1.13.0: 2016-06-20
---------------------------
-
-Added:
-- install.sh script to install pipeline and its Perl dependencies
-- Documentation for Bayesian identity check
-
-Changed:
-- Modified ready_workflow.pl to better align with user SOP
-- Use try/catch to handle unexpected errors in retrieving QC plex results
-from iRODS
-- Updated reference genome for Sequenom iRODS query
-- Update perl-irods-wrap dependency to 2.4.0; removes unhelpful warning
-messages to STDERR. This in turn requires baton version >= 0.16.4.
-
-Removed:
-- Script publish_infinium_file_list.pl; superseded by other publish scripts
-
-
-Release 1.12.1: 2016-05-13
---------------------------
-
-Fixed:
-- Support repeat scans from Infinium database
-
-
 Release 1.12.0: 2016-04-07
 --------------------------
 
diff --git a/src/perl/MANIFEST b/src/perl/MANIFEST
index 34b59fb08..781a32737 100644
--- a/src/perl/MANIFEST
+++ b/src/perl/MANIFEST
@@ -21,6 +21,7 @@ bin/publish_infinium_analysis.pl
 bin/publish_infinium_genotypes.pl
 bin/publish_sequenom_genotypes.pl
 bin/publish_snpset.pl
+bin/qc_fluidigm.pl
 bin/query_project_samples.pl
 bin/ready_external.pl
 bin/ready_infinium.pl
@@ -113,6 +114,7 @@ lib/WTSI/NPG/Genotyping/Fluidigm/AssayResultSet.pm
 lib/WTSI/NPG/Genotyping/Fluidigm/Collector.pm
 lib/WTSI/NPG/Genotyping/Fluidigm/ExportFile.pm
 lib/WTSI/NPG/Genotyping/Fluidigm/Publisher.pm
+lib/WTSI/NPG/Genotyping/Fluidigm/QC.pm
 lib/WTSI/NPG/Genotyping/Fluidigm/ResultSet.pm
 lib/WTSI/NPG/Genotyping/Fluidigm/Subscriber.pm
 lib/WTSI/NPG/Genotyping/GenderMarker.pm
@@ -354,6 +356,11 @@ t/fluidigm_publisher/repub/0123456789/0123456789.csv
 t/fluidigm_publisher/repub/0123456789/Data/aramis.tif
 t/fluidigm_publisher/repub/0123456789/Data/athos.tif
 t/fluidigm_publisher/repub/0123456789/Data/porthos.tif
+t/fluidigm_qc.t
+t/fluidigm_qc/1381735059/S01_1381735059.csv
+t/fluidigm_qc/1381735059/S02_1381735059.csv
+t/fluidigm_qc/fluidigm_qc.csv
+t/fluidigm_qc/fluidigm_qc_outdated_md5.csv
 t/fluidigm_resultset.t
 t/fluidigm_resultset/complete/0123456789/0123456789.csv
 t/fluidigm_resultset/complete/0123456789/Data/aramis.tif
@@ -708,6 +715,7 @@ t/WTSI/NPG/Genotyping/Fluidigm/AssayResultSetTest.pm
 t/WTSI/NPG/Genotyping/Fluidigm/AssayResultTest.pm
 t/WTSI/NPG/Genotyping/Fluidigm/ExportFileTest.pm
 t/WTSI/NPG/Genotyping/Fluidigm/PublisherTest.pm
+t/WTSI/NPG/Genotyping/Fluidigm/QCTest.pm
 t/WTSI/NPG/Genotyping/Fluidigm/ResultSetTest.pm
 t/WTSI/NPG/Genotyping/Fluidigm/SubscriberTest.pm
 t/WTSI/NPG/Genotyping/GenderMarkerCallTest.pm
diff --git a/src/perl/bin/qc_fluidigm.pl b/src/perl/bin/qc_fluidigm.pl
new file mode 100755
index 000000000..c54e638ea
--- /dev/null
+++ b/src/perl/bin/qc_fluidigm.pl
@@ -0,0 +1,301 @@
+#!/usr/bin/env perl
+
+package main;
+
+use strict;
+use warnings;
+use Cwd qw(abs_path);
+use File::Copy qw(cp);
+use File::Temp qw(tempfile);
+use File::Spec::Functions qw(tmpdir);
+use Getopt::Long;
+use Log::Log4perl qw(:levels);
+use Pod::Usage;
+
+use WTSI::DNAP::Utilities::ConfigureLogger qw(log_init);
+use WTSI::NPG::Genotyping::Fluidigm::AssayDataObject;
+use WTSI::NPG::Genotyping::Fluidigm::QC;
+use WTSI::NPG::iRODS;
+use WTSI::NPG::Utilities qw(user_session_log);
+
+my $uid = `whoami`;
+chomp($uid);
+my $session_log = user_session_log($uid, 'qc_fluidigm');
+
+our $VERSION = '';
+
+run() unless caller();
+
+sub run {
+    my $debug;
+    my $in_place;
+    my $log4perl_config;
+    my $new_csv;
+    my $old_csv;
+    my $query_path;
+    my $verbose;
+    my @filter_key;
+    my @filter_value;
+    my $stdio;
+
+    GetOptions('debug'          => \$debug,
+               'filter-key=s'   => \@filter_key,
+               'filter-value=s' => \@filter_value,
+               'help'           => sub { pod2usage(-verbose => 2,
+                                                   -exitval => 0) },
+               'in-place'       => \$in_place,
+               'logconf=s'      => \$log4perl_config,
+               'new-csv=s'      => \$new_csv,
+               'old-csv=s'      => \$old_csv,
+               'query-path=s'   => \$query_path,
+               'verbose'        => \$verbose,
+               ''               => \$stdio); # Permits trailing '-' for STDIN
+
+    # validate command line options and populate filter
+    my @filter;
+    if ($stdio) {
+        if ($query_path or @filter_key) {
+            pod2usage(-msg => "The --query-path and --filter-key options ".
+                      "are incompatible with reading from STDIN\n",
+                      -exitval => 2);
+        }
+    } else {
+        if (! defined $query_path) {
+             pod2usage(-msg => "If inputs are not supplied on STDIN, must ".
+                       "specify --query-path\n",
+                       -exitval => 2);
+        }
+        if (scalar @filter_key != scalar @filter_value) {
+            pod2usage(-msg => "There must be equal numbers of filter keys " .
+                          "and values\n",
+                      -exitval => 2);
+        }
+        while (@filter_key) {
+            push @filter, [pop @filter_key, pop @filter_value];
+        }
+    }
+    if ($in_place) {
+        if (defined $new_csv) {
+            pod2usage(-msg => "The --new-csv and --in-place options ".
+                          "are incompatible\n",
+                      -exitval => 2);
+        } elsif (! defined $old_csv) {
+            pod2usage(-msg => "The --old-csv option is required for ".
+                          "--in-place",
+                      -exitval => 2);
+        } else {
+            $new_csv = $old_csv;
+        }
+    }
+    # set up logging
+    my @log_levels;
+    if ($debug) { push @log_levels, $DEBUG; }
+    if ($verbose) { push @log_levels, $INFO; }
+    log_init(config => $log4perl_config,
+             file   => $session_log,
+             levels => \@log_levels);
+    my $log = Log::Log4perl->get_logger('main');
+
+    # Get input Fluidigm paths from STDIN or iRODS
+    my $irods = WTSI::NPG::iRODS->new();
+    my @fluidigm_data;
+    if ($stdio) {
+        while (my $line = <>) {
+            chomp $line;
+            push @fluidigm_data, $line;
+        }
+    } else {
+        @fluidigm_data =
+            $irods->find_objects_by_meta($query_path,
+                                         [fluidigm_plate => '%', 'like'],
+                                         [fluidigm_well  => '%', 'like'],
+                                         [type           => 'csv'],
+                                         @filter);
+    }
+    $log->info("Received ", scalar @fluidigm_data,
+               " Fluidigm data object paths");
+
+    # Find output filehandle
+    my $fh;
+    my $temp;
+    if (defined $new_csv) {
+        if (defined $old_csv && abs_path($old_csv) eq abs_path($new_csv)) {
+            ($fh, $temp) = tempfile('qc_fluidigm_XXXXXX',
+                                    DIR    => tmpdir(),
+                                    UNLINK => 1, # delete on script exit
+                                );
+            $log->debug("Created temporary file $temp for CSV output");
+        } else {
+            open $fh, ">", $new_csv ||
+                $log->logcroak("Cannot open output '", $new_csv, "'");
+            $log->debug("Opened path $new_csv for CSV output");
+        }
+    } else {
+        $log->debug("Writing output to STDOUT");
+        $fh = *STDOUT;
+    }
+    # Write updated QC results
+    my %args = (
+        data_object_paths => \@fluidigm_data,
+    );
+    if (defined $old_csv) { $args{'csv_path'} = $old_csv; }
+    my $qc = WTSI::NPG::Genotyping::Fluidigm::QC->new(\%args);
+    $qc->write_csv($fh);
+    if (defined $new_csv) {
+        close $fh || $log->logcroak("Cannot close CSV output");
+    }
+    if (defined $temp) {
+        my $cp_ok = cp($temp, $new_csv);
+        if ($cp_ok) {
+            $log->debug('Copied temporary file ', $temp, ' to ', $new_csv);
+        } else {
+            $log->logcroak('Failed to copy temporary file ', $temp,
+                           'to ', $new_csv);
+        }
+    }
+}
+
+__END__
+
+=head1 NAME
+
+qc_fluidigm
+
+=head1 SYNOPSIS
+
+Options:
+
+  --filter-key   Additional filter to limit set of dataObjs acted on.
+  --filter-value
+  --help         Display help.
+  --in-place     If given, write QC results to the file specified by
+                 --old-csv. Raises an error if --old-csv is not supplied.
+                 Incompatible with --new-csv.
+  --logconf      A log4perl configuration file. Optional.
+  --new-csv      Path of a CSV file for QC output. Optional; if --new-csv
+                 and --in-place are not given, output will be written
+                 to STDOUT.
+  --old-csv      Path of a CSV file from which to read existing QC records.
+                 Optional.
+  --query-path   An iRODS path to query for Fluidigm DataObjects. Required,
+                 unless iRODS paths are supplied on STDIN using the '-'
+                 option.
+  --verbose      Print messages while processing. Optional.
+
+=head1 DESCRIPTION
+
+Read published Fluidigm genotyping data from iRODS; cross-reference
+with existing QC records, if any; and write updated QC records in CSV
+format.
+
+=head2 Input
+
+=head3 Fluidigm data
+
+Input data from iRODS may be found via a metadata query, or from paths
+given on STDIN. Note that if data on iRODS is changed while the script
+is running, the changes will not necessarily appear in the output.
+
+=over
+
+=item *
+
+To query iRODS metadata, specify a search path using the --query-path option.
+The default query is for data objects with 'fluidigm_plate' and
+'fluidigm_well' attributes, and a 'type' attribute with value 'csv'.
+Additional query keys and values may be specified with the --filter-key
+and --filter-value options.
+
+=item *
+
+To read from STDIN, terminate the command line with the '-' option. In
+this mode, the --query-path, --filter-key and --filter-value options
+are invalid.
+
+=back
+
+=head3 Existing QC results
+
+If desired, specify existing QC results using the --old-csv option.
+
+CSV records are identified by their plate and well. If a record in the
+existing CSV has the same plate and well as one of the input iRODS data
+objects, and a different md5 checksum, it will be replaced with a record
+generated from the data object. Otherwise, the original record is output
+unchanged. Order of the existing CSV results is preserved.
+
+If an input data object does not appear in the existing CSV, a record for
+it will be appended to the output. If no existing CSV path is given, the
+script will simply write CSV output for all the inputs.
+
+=head2 Output
+
+=head3 CSV fields
+
+=over
+
+=item 1. Sample identifier
+
+=item 2. Call rate: Defined as field (9) / field (8), if field (8) is non-zero; zero otherwise.
+
+=item 3. Size of resultset (total assay results)
+
+=item 4. Total calls
+
+=item 5. Total controls
+
+=item 6. Total empty
+
+=item 7. Total valid
+
+=item 8. Total template assays: Defined as assays which are not empty and not controls.
+
+=item 9. Total template calls: Defined as template assays in (8) which are calls.
+
+=item 10. Fluidigm plate
+
+=item 11. Fluidigm well
+
+=item 12. md5 checksum
+
+=back
+
+Items 1 through 9 are taken from the fluidigm assay result file, while 10
+through 12 are from iRODS metadata.
+
+=head3 Output location
+
+=over
+
+=item * If the --in-place option is given, the script will replace the existing CSV file given by --old-csv.
+
+=item * If the --new-csv option is supplied, the script will write to the given file.
+
+=item * If neither option is given, results will be written to STDOUT.
+
+=back
+
+
+=head1 METHODS
+
+None
+
+=head1 AUTHOR
+
+Iain Bancarz <ib5@sanger.ac.uk>
+
+=head1 COPYRIGHT AND DISCLAIMER
+
+Copyright (c) 2017 Genome Research Limited. All Rights Reserved.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the Perl Artistic License or the GNU General
+Public License as published by the Free Software Foundation, either
+version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+=cut
diff --git a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResult.pm b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResult.pm
index 325a6a92f..a081b1c02 100644
--- a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResult.pm
+++ b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResult.pm
@@ -119,6 +119,42 @@ sub is_call {
           $self->converted_call ne $NO_CALL);
 }
 
+=head2 is_template_assay
+
+  Arg [1]    : None
+
+  Example    : $result->is_template
+  Description: Return True if is_empty and is_control are both false, ie.
+               the assay contains an experimental sample (also known as a
+               template).
+
+  Returntype : Bool
+
+=cut
+
+sub is_template_assay {
+ my ($self) = @_;
+
+ return !($self->is_empty() || $self->is_control());
+}
+
+=head2 is_template_call
+
+  Arg [1]    : None
+
+  Example    : $result->is_template_call
+  Description: Return True if is_template and is_call are both true.
+
+  Returntype : Bool
+
+=cut
+
+sub is_template_call {
+ my ($self) = @_;
+
+ return $self->is_template_assay() && $self->is_call();
+}
+
 =head2 is_valid
 
   Arg [1]    : None
diff --git a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResultSet.pm b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResultSet.pm
index 155c756d7..b294dd847 100644
--- a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResultSet.pm
+++ b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/AssayResultSet.pm
@@ -24,6 +24,73 @@ has 'assay_results' =>
    builder  => '_build_assay_results',
    lazy     => 1);
 
+has 'call_rate' =>
+  (is       => 'ro',
+   isa      => 'Num',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_call_rate',
+   documentation => 'QC metric, defined as total_template_calls / '.
+       'total_template_assays. Measures the call rate excluding control '.
+       'and empty assays.',
+);
+
+has 'total_calls' =>
+  (is       => 'ro',
+   isa      => 'Int',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_total_calls',
+   documentation => 'Number of assay results for which is_call is True',
+);
+
+has 'total_controls' =>
+  (is       => 'ro',
+   isa      => 'Int',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_total_controls',
+   documentation => 'Number of assay results for which is_control is True',
+);
+
+has 'total_empty' =>
+  (is       => 'ro',
+   isa      => 'Int',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_total_empty',
+   documentation => 'Number of assay results for which is_empty is True',
+);
+
+has 'total_template_assay_calls' =>
+  (is       => 'ro',
+   isa      => 'Int',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_total_template_assay_calls',
+   documentation => 'Number of assay results for which '.
+       'is_template_call is True',
+);
+
+has 'total_template_assays' =>
+  (is       => 'ro',
+   isa      => 'Int',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_total_template_assays',
+   documentation => 'Number of assay results for which '.
+       'is_template_assay is True',
+);
+
+has 'total_valid' =>
+  (is       => 'ro',
+   isa      => 'Int',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_total_valid',
+   documentation => 'Number of assay results for which is_valid is True',
+);
+
 around BUILDARGS => sub {
   my ($orig, $class, @args) = @_;
 
@@ -185,6 +252,62 @@ sub filter_on_confidence {
   return \@filtered_results;
 }
 
+
+=head2 summary_fields
+
+  Arg [1]    : None
+
+  Example    : $summary_fields = $result->summary_fields();
+  Description: Return an ArrayRef containing summary values. Call rate is
+               rounded to 4 decimal places for subsequent output. The
+               string 'NA' denotes an empty sample ID, which may occur
+               for an empty well.
+  Returntype : ArrayRef
+
+=cut
+
+sub summary_fields {
+  my ($self) = @_;
+
+  my $id_string = $self->canonical_sample_id() || 'NA';
+
+  my @fields = (
+    $id_string,
+    sprintf("%.4f", $self->call_rate),
+    $self->size(),
+    $self->total_calls,
+    $self->total_controls,
+    $self->total_empty,
+    $self->total_valid,
+    $self->total_template_assays,
+    $self->total_template_assay_calls,
+  );
+  return \@fields;
+}
+
+=head2 summary_string
+
+  Arg [1]    : None
+
+  Example    : $summary_string = $result->summary_string();
+  Description: Return a comma-separated string containing summary values,
+               same as those returned by summary_fields().
+  Returntype : Str
+
+=cut
+
+sub summary_string {
+  my ($self) = @_;
+  my $csv = Text::CSV->new ({ binary => 1 });
+  $csv->combine(@{$self->summary_fields()});
+  my $string = $csv->string();
+  if (! defined $string) {
+    $self->logconfess("Unable to generate CSV string from input '",
+                      $csv->error_input, "'");
+  }
+  return $string;
+}
+
 sub _build_assay_results {
   my ($self) = @_;
 
@@ -208,6 +331,57 @@ sub _build_assay_results {
   return $records;
 }
 
+sub _build_call_rate {
+  my ($self,) = @_;
+  my $call_rate = 0;
+  if ($self->total_template_assays != 0) {
+    $call_rate =
+        $self->total_template_assay_calls / $self->total_template_assays;
+  }
+  return $call_rate;
+}
+
+sub _build_total_calls {
+  my ($self,) = @_;
+  return $self->_count_matching_assays('is_call');
+}
+
+sub _build_total_controls {
+  my ($self,) = @_;
+  return $self->_count_matching_assays('is_control');
+}
+
+sub _build_total_empty {
+  my ($self,) = @_;
+  return $self->_count_matching_assays('is_empty');
+}
+
+sub _build_total_template_assay_calls {
+  my ($self,) = @_;
+  return $self->_count_matching_assays('is_template_call');
+}
+
+sub _build_total_template_assays {
+  my ($self,) = @_;
+  return $self->_count_matching_assays('is_template_assay');
+}
+
+sub _build_total_valid {
+  my ($self,) = @_;
+  return $self->_count_matching_assays('is_valid');
+}
+
+sub _count_matching_assays {
+  # method to count AssayResults which return True for a given object method
+  # eg. count instances of is_empty, is_call, is_invalid
+  my ($self, $sub_boolean) = @_;
+  my $count = 0;
+  foreach my $ar (@{$self->assay_results}) {
+    if ($ar->$sub_boolean()) { $count++; }
+  }
+  return $count;
+}
+
 sub _parse_assay_results {
   my ($self, $fh) = @_;
 
@@ -275,6 +449,7 @@ sub _parse_assay_results {
   return \@records;
 }
 
+
 __PACKAGE__->meta->make_immutable;
 
 no Moose;
@@ -294,11 +469,11 @@ for a number of SNPs.
 
 =head1 AUTHOR
 
-Keith James <kdj@sanger.ac.uk>
+Keith James <kdj@sanger.ac.uk>, Iain Bancarz <ib5@sanger.ac.uk>
 
 =head1 COPYRIGHT AND DISCLAIMER
 
-Copyright (C) 2014, 2015 Genome Research Limited. All Rights Reserved.
+Copyright (C) 2014, 2015, 2017 Genome Research Limited. All Rights Reserved.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the Perl Artistic License or the GNU General
diff --git a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/Collector.pm b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/Collector.pm
index d840177ad..1aca76d8e 100644
--- a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/Collector.pm
+++ b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/Collector.pm
@@ -1,9 +1,13 @@
 use utf8;
+use sigtrap qw/die untrapped normal-signals
+               stack-trace any error-signals/;
+# sigtrap ensures tempdir is deleted after control-C or similar
 
 package WTSI::NPG::Genotyping::Fluidigm::Collector;
 
 use DateTime;
-use File::Temp qw/tempdir/;
+use File::Temp;
+use File::Spec;
 use WTSI::NPG::iRODS;
 use WTSI::NPG::Utilities qw/md5sum/;
 
@@ -162,7 +166,8 @@ sub irods_publication_ok {
 
 sub _get_md5_by_address {
     my ($self, $export_file) = @_;
-    my $tmpdir = tempdir("fluidigm_samples_XXXXXX", CLEANUP => 1);
+    my $tmpdir = File::Temp->newdir("fluidigm_samples_XXXXXX",
+                                    dir => File::Spec->tmpdir() );
     my %md5_by_address;
     foreach my $address (@{$export_file->addresses}) {
         my $filename = $export_file->fluidigm_filename($address);
@@ -170,8 +175,9 @@ sub _get_md5_by_address {
         my $records = $export_file->write_assay_result_data($address, $file);
         my $md5 = md5sum($file);
         $md5_by_address{$address} = $md5;
-        $self->debug("Wrote $records records for address $address into ",
-                     "temp file '", $file, "', with md5 '", $md5, "'");
+        $self->debug("Wrote ", $records, " records for address ",
+                     $address, " into temp file ", $file,
+                     ", with md5 ", $md5);
     }
     return %md5_by_address;
 }
diff --git a/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/QC.pm b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/QC.pm
new file mode 100644
index 000000000..88ab02b8f
--- /dev/null
+++ b/src/perl/lib/WTSI/NPG/Genotyping/Fluidigm/QC.pm
@@ -0,0 +1,427 @@
+
+package WTSI::NPG::Genotyping::Fluidigm::QC;
+
+use Moose;
+
+use Set::Scalar;
+use Text::CSV;
+use Try::Tiny;
+
+use WTSI::NPG::iRODS;
+use WTSI::NPG::iRODS::Metadata;
+use WTSI::NPG::Genotyping::Fluidigm::AssayDataObject;
+
+our $VERSION = '';
+
+our $PLATE_INDEX = 9;
+our $WELL_INDEX = 10;
+our $MD5_INDEX = 11;
+our $EXPECTED_FIELDS_TOTAL = 12;
+
+our $REPORTING_BLOCK_SIZE = 1000;
+
+with 'WTSI::DNAP::Utilities::Loggable';
+
+has 'checksums_by_path' =>
+  (is       => 'ro',
+   isa      => 'HashRef[Str]',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_checksums_by_path',
+   documentation => 'The md5 checksum for each input iRODS path. ',
+);
+
+has 'csv' =>
+  (is       => 'ro',
+   isa      => 'Text::CSV',
+   init_arg => undef,
+   lazy     => 1,
+   default  => sub { return Text::CSV->new ({ binary => 1, }); },
+   documentation => 'Object for processing data in CSV format',
+);
+
+has 'csv_path' =>
+  (is       => 'ro',
+   isa      => 'Maybe[Str]',
+   documentation => 'Path for input of existing QC results. Optional; '.
+       'if not defined, omit CSV input.',
+);
+
+has 'data_object_paths' =>
+  (is       => 'ro',
+   isa      => 'ArrayRef[Str]',
+   required => 1,
+   documentation => 'iRODS paths for results which may be added to QC',
+);
+
+has 'irods' =>
+  (is       => 'ro',
+   isa      => 'WTSI::NPG::iRODS',
+   lazy     => 1,
+   builder  => '_build_irods',
+);
+
+has 'paths_by_plate_well' =>
+  (is       => 'ro',
+   isa      => 'HashRef[HashRef[Str]]',
+   init_arg => undef,
+   lazy     => 1,
+   builder  => '_build_paths_by_plate_well',
+   documentation => 'Input iRODS paths, indexed by plate and well. ',
+);
+
+
+=head2 csv_fields
+
+  Arg [1]    : WTSI::NPG::Genotyping::Fluidigm::AssayDataObject
+
+  Example    : my $fields = $qc->csv_update_fields($assay_data_object);
+
+  Description: Find QC data for the given AssayDataObject, for CSV output.
+
+               CSV format consists of the fields returned by the
+               summary_string() method of
+               WTSI::NPG::Genotyping::Fluidigm::AssayResultSet;
+               and three additional fields, denoting the Fluidigm
+               plate, Fluidigm well, and md5 checksum.
+
+  Returntype : [ArrayRef] CSV fields for update
+
+=cut
+
+sub csv_fields {
+    my ($self, $obj) = @_;
+    my @fields = @{$obj->assay_resultset->summary_fields};
+    # Find Fluidigm plate/well from object metadata
+    my ($plate, $well);
+    my $plate_avu = $obj->get_avu($FLUIDIGM_PLATE_NAME);
+    my $well_avu = $obj->get_avu($FLUIDIGM_PLATE_WELL);
+    if ($plate_avu) {
+        $plate = $plate_avu->{'value'};
+    } else {
+        $self->logcroak("$FLUIDIGM_PLATE_NAME AVU not found for data ",
+                        "object '", $obj->str, "'");
+    }
+    if ($well_avu) {
+        $well = $well_avu->{'value'};
+    } else {
+        $self->logcroak("$FLUIDIGM_PLATE_WELL AVU not found for data ",
+                        "object '", $obj->str, "'");
+    }
+    # Append plate, well, and md5 checksum
+    push @fields, $plate, $well, $obj->checksum;
+    return \@fields;
+}
+
+=head2 csv_string
+
+  Arg [1]    : WTSI::NPG::Genotyping::Fluidigm::AssayDataObject
+
+  Example    : my $str = $qc->csv_string($assay_data_object);
+  Description: Find updated QC data for the given AssayDataObject.
+               Return string for CSV output.
+  Returntype : Str
+
+=cut
+
+sub csv_string {
+    my ($self, $assay_data_object) = @_;
+    my $fields = $self->csv_fields($assay_data_object);
+    my $status = $self->csv->combine(@{$fields});
+    if (! defined $status) {
+        $self->logcroak("Error combining CSV inputs: '",
+                        $self->csv->error_input, "'");
+    }
+    return $self->csv->string();
+}
+
+=head2 rewrite_existing_csv
+
+  Arg [1]    : Filehandle
+
+  Example    : my $data_object_paths = $qc->rewrite_existing_csv($fh);
+
+  Description: Read the existing CSV file, and write an updated version to the
+               given filehandle. Records will be updated if there is a
+               matching data object with the same plate and well, and a
+               different checksum; otherwise the original record is output
+               unchanged.
+
+               Returns the set of data object paths which match
+               the plate and well of an existing CSV record.
+
+  Returntype : Set::Scalar
+
+=cut
+
+sub rewrite_existing_csv {
+    my ($self, $out) = @_;
+    my $existing_paths = Set::Scalar->new();
+    if (! defined $self->csv_path) {
+        $self->logwarn('Existing CSV path is not defined; cannot rewrite ',
+                       'previous results');
+        return $existing_paths;
+    }
+    my $matched = 0;
+    my $updated = 0;
+    my $total = 0;
+    open my $in, "<", $self->csv_path ||
+        $self->logcroak("Cannot open CSV path '", $self->csv_path, "'");
+    while (<$in>) {
+        my $original_csv_line = $_;
+        chomp;
+        my @fields = $self->_parse_csv_fields($_);
+        my $plate = $fields[$PLATE_INDEX];
+        my $well = $fields[$WELL_INDEX];
+        my $update_path = $self->paths_by_plate_well->{$plate}{$well};
+        if (defined $update_path) {
+            $existing_paths->insert($update_path);
+            $matched++;
+            my $md5 = $fields[$MD5_INDEX];
+            if ($md5 eq $self->checksums_by_path->{$update_path}) {
+                $self->debug('No update for plate ', $plate, ', well ',
+                             $well, '; md5 checksum is unchanged');
+                print $out $original_csv_line;
+            } else {
+                $self->debug('Updating plate ', $plate, ', well ',
+                             $well, ' from data object path',
+                             $update_path);
+                my $update_obj = $self->_get_fluidigm_data_obj($update_path);
+                print $out $self->csv_string($update_obj)."\n";
+                $updated++;
+            }
+        } else {
+            $self->debug('No update for plate ', $plate, ', well ',
+                         $well, '; no corresponding data object was found');
+            print $out $original_csv_line;
+        }
+        $total++;
+    }
+    close $in ||
+        $self->logcroak("Cannot close CSV path '", $self->csv_path, "'");
+    $self->info('Rewrote ', $total, ' existing CSV records for Fluidigm ',
+                'QC; matched ', $matched, ' data objects; updated ',
+                $updated, ' records');
+    return $existing_paths;
+}
+
+
+=head2 write_csv
+
+  Arg [1]    : Filehandle for output
+
+  Example    : $qc->write_csv($fh);
+
+  Description: Write an updated CSV to the given filehandle. Output
+               consists of records in the existing CSV file,
+               updated as appropriate; and records for any new data
+               objects which do not appear in the existing file. (If the
+               existing CSV file is not defined, this method simply writes
+               CSV records for all data objects.)
+
+               Output for new data objects is sorted in (plate, well) order.
+
+  Returntype : Returns True on completion
+
+=cut
+
+sub write_csv {
+    my ($self, $out) = @_;
+    my $existing_paths; # data object paths which match existing CSV records
+    if (defined $self->csv_path) {
+        $existing_paths = $self->rewrite_existing_csv($out);
+    }
+    my $total = 0;
+    my @update_lines;
+    foreach my $obj_path (@{$self->data_object_paths}) {
+        if (defined $existing_paths && $existing_paths->has($obj_path)) {
+            $self->debug('Object ', $obj_path, ' already exists in CSV');
+        } else {
+            $self->debug('Finding new CSV output for object ', $obj_path);
+            my $data_obj = $self->_get_fluidigm_data_obj($obj_path);
+            push @update_lines, $self->csv_string($data_obj)."\n";
+            $total++;
+        }
+    }
+    $self->info('Found ', $total, ' new CSV records for Fluidigm QC');
+    my $sort_ref = $self->_by_plate_well();
+    my @sorted_lines = sort $sort_ref @update_lines;
+    $self->debug('Sorted ', $total, ' new records in (plate, well) order');
+    foreach my $line (@sorted_lines) { print $out $line; }
+    $self->debug('Wrote ', $total, ' new records to output');
+    return 1;
+}
+
+{
+    # Block structure enables %meta_by_path to be shared between two
+    # builder methods. This allows metadata to be gathered on only one
+    # pass through iRODS, while at the same time having lazy attributes.
+
+    my %meta_by_path;
+
+    sub _populate_meta_by_path {
+        my ($self,) = @_;
+        my $total = scalar @{$self->data_object_paths};
+        $self->info('Finding (checksum, plate, well) metadata for ', $total,
+                    ' data object paths');
+        my $count = 0;
+        foreach my $obj_path (@{$self->data_object_paths}) {
+            my $data_obj = $self->_get_fluidigm_data_obj($obj_path);
+            my $checksum = $data_obj->checksum;
+            my $plate = $data_obj->get_avu($FLUIDIGM_PLATE_NAME)->{'value'};
+            my $well = $data_obj->get_avu($FLUIDIGM_PLATE_WELL)->{'value'};
+            $meta_by_path{$obj_path} = [$checksum, $plate, $well];
+            $count++;
+            if ($count % $REPORTING_BLOCK_SIZE == 0) {
+                $self->debug('Found (plate, well) index and checksum for ',
+                             $count, ' of ', $total, ' data object paths');
+            }
+        }
+        $self->info('Finished processing ', $total, ' data object paths');
+        return 1;
+    }
+
+    sub _build_checksums_by_path {
+        my ($self,) = @_;
+        if (! %meta_by_path) {
+            $self->debug('No metadata found for checksums; ',
+                         'populating from iRODS');
+            $self->_populate_meta_by_path();
+        }
+        my %checksums_by_path;
+        foreach my $obj_path (@{$self->data_object_paths}) {
+            my $values = $meta_by_path{$obj_path};
+            my ($checksum, $plate, $well) = @{$values};
+            if (defined $checksums_by_path{$obj_path}) {
+                $self->logcroak('iRODS data object path ', $obj_path,
+                                ' appears more than once in inputs');
+            }
+            $checksums_by_path{$obj_path} = $checksum;
+        }
+        return \%checksums_by_path;
+    }
+
+    sub _build_paths_by_plate_well {
+        my ($self,) = @_;
+        if (! %meta_by_path) {
+            $self->debug('No metadata found for plate/well; ',
+                         'populating from iRODS');
+            $self->_populate_meta_by_path();
+        }
+        my %paths_by_plate_well;
+        foreach my $obj_path (@{$self->data_object_paths}) {
+            my $values = $meta_by_path{$obj_path};
+            my ($checksum, $plate, $well) = @{$values};
+            if (defined $paths_by_plate_well{$plate}{$well}) {
+                $self->logcroak('Duplicate plate ', $plate, ' and well ',
+                                $well, ' for data objects: ', $obj_path, ', ',
+                                $paths_by_plate_well{$plate}{$well}
+                            );
+            }
+            $paths_by_plate_well{$plate}{$well} = $obj_path;
+        }
+        return \%paths_by_plate_well;
+    }
+}
+
+sub _build_irods {
+    # use instead of a default, to allow irods attribute to be lazy
+    my ($self,) = @_;
+    return WTSI::NPG::iRODS->new;
+}
+
+sub _by_plate_well {
+    # return a coderef used to sort CSV lines in (plate, well) order
+    my ($self,) = @_;
+
+    return sub {
+        my @fields_a = $self->_parse_csv_fields($a);
+	my @fields_b = $self->_parse_csv_fields($b);
+	my $plate_a = $fields_a[$PLATE_INDEX];
+	my $plate_b = $fields_b[$PLATE_INDEX];
+	my $well_a = $fields_a[$WELL_INDEX];
+	my $well_b = $fields_b[$WELL_INDEX];
+	my @well_fields_a = split(/S[0]*/msx, $well_a);
+	my $well_num_a = pop @well_fields_a;
+	my @well_fields_b = split(/S[0]*/msx, $well_b);
+	my $well_num_b = pop @well_fields_b;
+
+	return $plate_a <=> $plate_b || $well_num_a <=> $well_num_b;
+    };
+}
+
+sub _get_fluidigm_data_obj {
+    # safely create a Fluidigm AssayDataObject from path
+    my ($self, $obj_path) = @_;
+    my $data_obj;
+    try {
+        $data_obj = WTSI::NPG::Genotyping::Fluidigm::AssayDataObject->new
+            ($self->irods, $obj_path);
+    } catch {
+        $self->logcroak("Unable to create Fluidigm DataObject from ",
+                        "iRODS path '", $obj_path, "': $_");
+    };
+    return $data_obj;
+}
+
+sub _parse_csv_fields {
+    my ($self, $input) = @_;
+    # parse input string and check it is a valid Fluidigm QC record
+    $self->csv->parse($input);
+    my @fields = $self->csv->fields();
+    if (! @fields) {
+        $self->logcroak("Unable to parse CSV input: '",
+                        $self->csv->error_input(), "'");
+    } elsif (scalar @fields != $EXPECTED_FIELDS_TOTAL) {
+        $self->logcroak("Expected ", $EXPECTED_FIELDS_TOTAL,
+                        " fields, found ", scalar @fields,
+                        " from input: ", $input);
+    }
+    return @fields;
+}
+
+
+__PACKAGE__->meta->make_immutable;
+
+no Moose;
+
+1;
+
+
+__END__
+
+=head1 NAME
+
+WTSI::NPG::Genotyping::Fluidigm::QC
+
+=head1 DESCRIPTION
+
+A class to process quality control metrics for Fluidigm results.
+
+Find QC metric values from iRODS for CSV output. Optionally, can supply a
+CSV file with existing QC records, which will be updated if the checksum of
+the corresponding iRODS data object has changed.
+
+Output consists of any existing records in their original order, followed
+by new records in (plate, well) order. Each (plate, well) pair will have
+exactly one record in the output.
+
+=head1 AUTHOR
+
+Iain Bancarz <ib5@sanger.ac.uk>
+
+=head1 COPYRIGHT AND DISCLAIMER
+
+Copyright (C) 2017 Genome Research Limited. All Rights Reserved.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the Perl Artistic License or the GNU General
+Public License as published by the Free Software Foundation, either
+version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+=cut
diff --git a/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultSetTest.pm b/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultSetTest.pm
index 09564aec1..2d23ee472 100644
--- a/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultSetTest.pm
+++ b/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultSetTest.pm
@@ -8,7 +8,7 @@ use warnings;
 
 use base qw(WTSI::NPG::Test);
 use File::Spec;
-use Test::More tests => 68;
+use Test::More tests => 70;
 use Test::Exception;
 
 Log::Log4perl::init('./etc/log4perl_tests.conf');
@@ -96,6 +96,19 @@ sub size : Test(1) {
   cmp_ok($resultset->size, '==', 96, 'Expected size');
 }
 
+sub string : Test(1) {
+  cmp_ok($resultset->summary_string(),
+         'eq',
+         'ABC0123456789,1.0000,96,96,70,70,96,26,26',
+         'Expected CSV string');
+}
+
+sub summary_fields : Test(1) {
+  my $expected_fields =
+      ['ABC0123456789', '1.0000', 96, 96, 70, 70, 96, 26, 26];
+  is_deeply($resultset->summary_fields, $expected_fields, 'Expected summary');
+}
+
 sub assay_results : Test(3) {
   cmp_ok(scalar @{$resultset->assay_results}, '==', 96,
          'Contains expected number of assay results');
diff --git a/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultTest.pm b/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultTest.pm
index 7927f7e2e..635d2a3a1 100644
--- a/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultTest.pm
+++ b/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/AssayResultTest.pm
@@ -8,7 +8,7 @@ use warnings;
 
 use base qw(WTSI::NPG::Test);
 use File::Spec;
-use Test::More tests => 402;
+use Test::More tests => 407;
 use Test::Exception;
 
 Log::Log4perl::init('./etc/log4perl_tests.conf');
@@ -244,6 +244,91 @@ sub is_call : Test(5) {
       str            => '')->is_call, 'Is not call 3');
 }
 
+sub is_template : Test(5) {
+
+    # AssayResult is a template assay iff not empty and not control
+    ok(WTSI::NPG::Genotyping::Fluidigm::AssayResult->new
+     (assay          => 'S01-A01',
+      snp_assayed    => 'rs0123456',
+      x_allele       => 'G',
+      y_allele       => 'T',
+      sample_name    => 'ABC0123456789',
+      type           => 'Unknown',
+      auto           => 'XY',
+      confidence     => 0.1,
+      final          => 'XY',
+      converted_call => 'G:T',
+      x_intensity    => 0.1,
+      y_intensity    => 0.1,
+      str            => '')->is_template_assay, 'Is template assay 1');
+
+    # Empty AssayResult is not a template assay
+    ok(!WTSI::NPG::Genotyping::Fluidigm::AssayResult->new
+     (assay          => 'S01-A01',
+      snp_assayed    => 'rs0123456',
+      x_allele       => 'G',
+      y_allele       => 'T',
+      sample_name    => '[ Empty ]',
+      type           => 'Unknown',
+      auto           => 'XY',
+      confidence     => 0.1,
+      final          => 'XY',
+      converted_call => 'G:T',
+      x_intensity    => 0.1,
+      y_intensity    => 0.1,
+      str            => '')->is_template_assay, 'Is template assay 2');
+
+    # Control AssayResult is not a template assay
+    ok(!WTSI::NPG::Genotyping::Fluidigm::AssayResult->new
+     (assay          => 'S01-A01',
+      snp_assayed    => '',
+      x_allele       => 'G',
+      y_allele       => 'T',
+      sample_name    => 'ABC0123456789',
+      type           => 'NTC',
+      auto           => 'XY',
+      confidence     => 0.1,
+      final          => 'XY',
+      converted_call => 'G:T',
+      x_intensity    => 0.1,
+      y_intensity    => 0.1,
+      str            => '')->is_template_assay, 'Is template assay 3');
+
+    # AssayResult is a template assay *and* a call
+    ok(WTSI::NPG::Genotyping::Fluidigm::AssayResult->new
+     (assay          => 'S01-A01',
+      snp_assayed    => 'rs0123456',
+      x_allele       => 'G',
+      y_allele       => 'T',
+      sample_name    => 'ABC0123456789',
+      type           => 'Unknown',
+      auto           => 'XY',
+      confidence     => 0.1,
+      final          => 'XY',
+      converted_call => 'G:T',
+      x_intensity    => 0.1,
+      y_intensity    => 0.1,
+      str            => '')->is_template_call, 'Is template call 1');
+
+    # AssayResult is a template assay *and not* a call
+    ok(!WTSI::NPG::Genotyping::Fluidigm::AssayResult->new
+     (assay          => 'S01-A01',
+      snp_assayed    => 'rs0123456',
+      x_allele       => 'G',
+      y_allele       => 'T',
+      sample_name    => 'ABC0123456789',
+      type           => 'Unknown',
+      auto           => 'XY',
+      confidence     => 0.1,
+      final          => 'No Call',
+      converted_call => 'No Call',
+      x_intensity    => 0.1,
+      y_intensity    => 0.1,
+      str            => '')->is_template_call, 'Is template call 2');
+
+}
+
+
 sub is_valid : Test(4) {
   # Evaluate whether a result is valid. See is_call. 'No Call' and 'invalid'
   # are distinct and represent different experimental outcomes.
diff --git a/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/QCTest.pm b/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/QCTest.pm
new file mode 100644
index 000000000..92be8a445
--- /dev/null
+++ b/src/perl/t/WTSI/NPG/Genotyping/Fluidigm/QCTest.pm
@@ -0,0 +1,227 @@
+use utf8;
+
+package WTSI::NPG::Genotyping::Fluidigm::QCTest;
+
+use strict;
+use warnings;
+
+use base qw(WTSI::NPG::Test);
+use File::Copy qw/copy/;
+use File::Slurp qw/read_file/;
+use File::Temp qw/tempdir/;
+use Set::Scalar;
+use Test::More tests => 17;
+use Test::Exception;
+use Text::CSV;
+
+our $logconf = './etc/log4perl_tests.conf';
+Log::Log4perl::init($logconf);
+our $log = Log::Log4perl->get_logger();
+
+BEGIN { use_ok('WTSI::NPG::Genotyping::Fluidigm::QC'); }
+
+use WTSI::NPG::Genotyping::Fluidigm::AssayDataObject;
+use WTSI::NPG::Genotyping::Fluidigm::QC;
+use WTSI::NPG::iRODS;
+use WTSI::NPG::iRODS::Metadata; # has attribute name constants
+use WTSI::NPG::Utilities qw(md5sum);
+
+my $script = 'qc_fluidigm.pl';
+my $plate = '1381735059';
+my $data_path = "./t/fluidigm_qc/$plate";
+my $irods_tmp_coll;
+my @irods_paths;
+my $pid = $$;
+my $tmp;
+my $csv_name = 'fluidigm_qc.csv';
+my $csv_name_outdated = 'fluidigm_qc_outdated_md5.csv';
+
+sub make_fixture : Test(setup) {
+    $tmp = tempdir('Fluidigm_QC_test_XXXXXX', CLEANUP => 1 );
+    copy("./t/fluidigm_qc/$csv_name", $tmp);
+    copy("./t/fluidigm_qc/$csv_name_outdated", $tmp);
+    my $irods = WTSI::NPG::iRODS->new;
+    $irods_tmp_coll = $irods->add_collection("FluidigmQCTest.$pid");
+    $irods->put_collection($data_path, $irods_tmp_coll);
+    foreach my $well (qw/S01 S02/) {
+        my $name = $well.'_'.$plate.'.csv';
+        my $irods_path = $irods_tmp_coll.'/'.$plate.'/'.$name;
+        $irods->add_object_avu($irods_path, 'type', 'csv');
+        $irods->add_object_avu($irods_path, $FLUIDIGM_PLATE_NAME, $plate);
+        $irods->add_object_avu($irods_path, $FLUIDIGM_PLATE_WELL, $well);
+        push @irods_paths, $irods_path;
+    }
+}
+
+sub teardown : Test(teardown) {
+    @irods_paths = ();
+    my $irods = WTSI::NPG::iRODS->new;
+    $irods->remove_collection($irods_tmp_coll);
+}
+
+sub require : Test(1) {
+    require_ok('WTSI::NPG::Genotyping::Fluidigm::QC');
+}
+
+sub csv_output : Test(5) {
+    my $qc = _create_qc_object();
+    my $irods = WTSI::NPG::iRODS->new;
+    my @data_objects;
+    foreach my $obj_path (@irods_paths) {
+        my $obj = WTSI::NPG::Genotyping::Fluidigm::AssayDataObject->new
+            ($irods, $obj_path);
+        push @data_objects, $obj;
+    }
+    my $fields;
+    lives_ok(sub {$fields = $qc->csv_fields($data_objects[1]); },
+             'CSV fields found OK');
+    my $expected_fields = [
+        'XYZ0987654321',
+        '0.9231',
+        96,
+        94,
+        70,
+        70,
+        96,
+        26,
+        24,
+        '1381735059',
+        'S02',
+        '73ca301a0a9e1b9cf87d4daf59eb2815',
+    ];
+    is_deeply($fields, $expected_fields,
+              'Field contents match expected values');
+    my $string;
+    lives_ok(sub {$string = $qc->csv_string($data_objects[1]); },
+             'CSV string found OK');
+    my $expected_string = 'XYZ0987654321,0.9231,96,94,70,70,96,26,24,'.
+        '1381735059,S02,73ca301a0a9e1b9cf87d4daf59eb2815';
+    ok($string eq $expected_string,
+       'CSV string contents match expected values');
+
+    $data_objects[0]->remove_avu($FLUIDIGM_PLATE_WELL, 'S01');
+    dies_ok(sub { $qc->csv_fields($data_objects[0]); },
+            'Dies without required metadata');
+}
+
+sub rewrite_existing : Test(2) {
+    my $qc = _create_qc_object();
+    my $output_path = "$tmp/rewritten.csv";
+    open my $fh, ">", $output_path ||
+        $log->logcroak("Cannot open CSV output ", $output_path);
+    my $got_paths = $qc->rewrite_existing_csv($fh);
+    close $fh || $log->logcroak("Cannot close CSV output ", $output_path);
+    my $expected_paths = Set::Scalar->new();
+    my $path = $irods_tmp_coll.'/1381735059/S01_1381735059.csv';
+    $expected_paths->insert($path);
+    is_deeply($got_paths, $expected_paths, 'Data object paths match');
+    my $contents = read_file($output_path);
+    my $md5 = '11413e77cde2a8dcca89705fe5b25a2d';
+    my $expected = 'ABC0123456789,1.0000,96,96,70,70,96,26,26,1381735059'.
+        ",S01,$md5\n";
+    cmp_ok($contents, 'eq', $expected, 'Rewritten CSV file contents OK');
+}
+
+sub script_metaquery : Test(2) {
+    my $cmd = "$script --query-path $irods_tmp_coll ".
+        "--old-csv $tmp/$csv_name --in-place --logconf $logconf --debug";
+    $log->info("Running command '$cmd'");
+    ok(system($cmd)==0, "Script with --in-place and metaquery exits OK");
+    my $msg = 'Script in-place CSV output matches expected values';
+    _validate_csv_output("$tmp/$csv_name", $msg);
+}
+
+sub script_update : Test(2) {
+    # ensure an entry with outdated md5 checksum is replaced
+    my $cmd = "$script --query-path $irods_tmp_coll ".
+        "--old-csv $tmp/$csv_name_outdated ".
+            "--in-place --logconf $logconf --debug";
+    $log->info("Running command '$cmd'");
+    ok(system($cmd)==0, "Script with outdated input exits OK");
+    _validate_csv_output("$tmp/$csv_name_outdated",
+                         'Script updated md5 checksum in CSV');
+}
+
+sub script_stdin : Test(2) {
+    my $fh;
+    my $input_path = $tmp."/test_inputs.txt";
+    open $fh, ">", $input_path ||
+        $log->logcroak("Cannot open '$input_path'");
+    foreach my $path (@irods_paths) {
+        print $fh $path."\n";
+    }
+    close $fh || $log->logcroak("Cannot close '$input_path'");
+    my $new_csv = "$tmp/fluidigm_qc_output.csv";
+    my $cmd = "$script --new-csv $new_csv --old-csv $tmp/$csv_name ".
+        "--logconf $logconf - < $input_path";
+    $log->info("Running command '$cmd'");
+    ok(system($cmd)==0, "Script with STDIN and new CSV file exits OK");
+     _validate_csv_output($new_csv, 'Script CSV output OK, input from STDIN');
+}
+
+sub write_all : Test(2) {
+    my $qc = _create_qc_object();
+    my $output_path = "$tmp/qc_output.csv";
+    open my $fh, ">", $output_path ||
+        $log->logcroak("Cannot open CSV output ", $output_path);
+    ok($qc->write_csv($fh), 'write_csv method returns OK');
+    close $fh || $log->logcroak("Cannot close CSV output ", $output_path);
+    _validate_csv_output($output_path, 'CSV output from QC object OK');
+}
+
+sub _create_qc_object {
+    my $irods = WTSI::NPG::iRODS->new;
+    # 1 of the 2 AssayDataObjects is already present in fluidigm_qc.csv
+    # updated contents will contain QC results for the other AssayDataObject
+    my $csv_path = "$tmp/$csv_name";
+    my $qc = WTSI::NPG::Genotyping::Fluidigm::QC->new(
+        csv_path     => $csv_path,
+        data_object_paths => \@irods_paths,
+    );
+    return $qc;
+}
+
+sub _validate_csv_output {
+    # check that CSV output matches the expected values
+    # run an is_deeply test with the given message
+    my ($csv_path, $message, ) = @_;
+    # check the CSV output
+    my $csv = Text::CSV->new ( { binary => 1 } );
+    open my $fh, "<", "$csv_path" ||
+        $log->logcroak("Cannot open input '$csv_path'");
+    my $contents = $csv->getline_all($fh);
+    close $fh || $log->logcroak("Cannot close input '$csv_path'");
+    my $expected_contents = [
+        [
+            'ABC0123456789',
+            '1.0000',
+            96,
+            96,
+            70,
+            70,
+            96,
+            26,
+            26,
+            '1381735059',
+            'S01',
+            '11413e77cde2a8dcca89705fe5b25a2d',
+        ], [
+            'XYZ0987654321',
+            '0.9231',
+            96,
+            94,
+            70,
+            70,
+            96,
+            26,
+            24,
+            '1381735059',
+            'S02',
+            '73ca301a0a9e1b9cf87d4daf59eb2815',
+        ],
+    ];
+    is_deeply($contents, $expected_contents, $message);
+}
+
+
+1;
diff --git a/src/perl/t/fluidigm_qc.t b/src/perl/t/fluidigm_qc.t
new file mode 100644
index 000000000..70178d21e
--- /dev/null
+++ b/src/perl/t/fluidigm_qc.t
@@ -0,0 +1,9 @@
+
+use utf8;
+
+use strict;
+use warnings;
+
+use WTSI::NPG::Genotyping::Fluidigm::QCTest;
+
+WTSI::NPG::Genotyping::Fluidigm::QCTest->runtests;
diff --git a/src/perl/t/fluidigm_qc/1381735059/S01_1381735059.csv b/src/perl/t/fluidigm_qc/1381735059/S01_1381735059.csv
new file mode 100644
index 000000000..2ccdf591c
--- /dev/null
+++ b/src/perl/t/fluidigm_qc/1381735059/S01_1381735059.csv
@@ -0,0 +1,96 @@
+S01-A01	GS34251	T	C	ABC0123456789	Unknown	XY	100	XY	T:C	0.1	0.1
+S01-A02	GS34251	T	C	ABC0123456789	Unknown	XY	99	XY	T:C	0.1	0.1
+S01-A03	GS35220	C	T	ABC0123456789	Unknown	XY	98	XY	C:T	0.1	0.1
+S01-A04	GS35220	C	T	ABC0123456789	Unknown	XY	97	XY	C:T	0.1	0.1
+S01-A05	rs11096957	T	G	ABC0123456789	Unknown	XY	100	XY	T:G	0.1	0.1
+S01-A06	rs12828016	G	T	ABC0123456789	Unknown	XY	100	XY	G:T	0.1	0.1
+S01-A07	rs156697	A	G	ABC0123456789	Unknown	XY	100	XY	A:G	0.1	0.1
+S01-A08	rs1801262	T	C	ABC0123456789	Unknown	XY	100	XY	T:C	0.1	0.1
+S01-A09	rs1805034	C	T	ABC0123456789	Unknown	XY	100	XY	C:T	0.1	0.1
+S01-A10	rs1805087	A	G	ABC0123456789	Unknown	XY	100	XY	A:G	0.1	0.1
+S01-A11	rs2247870	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A12	rs2286963	T	G	ABC0123456789	Unknown	XY	100	XY	T:G	0.1	0.1
+S01-A13	rs3742207	T	G	ABC0123456789	Unknown	XY	100	XY	T:G	0.1	0.1
+S01-A14	rs3795677	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A15	rs4075254	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A16	rs4619	A	G	ABC0123456789	Unknown	XY	100	XY	A:G	0.1	0.1
+S01-A17	rs4843075	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A18	rs5215	C	T	ABC0123456789	Unknown	XY	100	XY	C:T	0.1	0.1
+S01-A19	rs6166	C	T	ABC0123456789	Unknown	XY	100	XY	C:T	0.1	0.1
+S01-A20	rs649058	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A21	rs6557634	T	C	ABC0123456789	Unknown	XY	100	XY	T:C	0.1	0.1
+S01-A22	rs6759892	T	G	ABC0123456789	Unknown	XY	100	XY	T:G	0.1	0.1
+S01-A23	rs7298565	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A24	rs753381	T	C	ABC0123456789	Unknown	XY	100	XY	T:C	0.1	0.1
+S01-A25	rs7627615	G	A	ABC0123456789	Unknown	XY	100	XY	G:A	0.1	0.1
+S01-A26	rs8065080	T	C	ABC0123456789	Unknown	XY	100	XY	T:C	0.1	0.1
+S01-A27				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A28				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A29				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A30				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A31				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A32				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A33				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A34				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A35				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A36				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A37				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A38				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A39				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A40				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A41				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A42				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A43				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A44				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A45				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A46				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A47				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A48				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A49				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A50				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A51				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A52				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A53				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A54				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A55				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A56				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A57				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A58				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A59				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A60				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A61				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A62				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A63				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A64				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A65				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A66				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A67				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A68				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A69				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A70				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A71				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A72				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A73				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A74				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A75				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A76				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A77				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A78				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A79				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A80				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A81				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A82				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A83				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A84				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A85				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A86				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A87				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A88				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A89				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A90				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A91				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A92				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A93				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A94				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A95				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S01-A96				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
diff --git a/src/perl/t/fluidigm_qc/1381735059/S02_1381735059.csv b/src/perl/t/fluidigm_qc/1381735059/S02_1381735059.csv
new file mode 100644
index 000000000..4738b4532
--- /dev/null
+++ b/src/perl/t/fluidigm_qc/1381735059/S02_1381735059.csv
@@ -0,0 +1,96 @@
+S02-A01	GS34251	T	C	XYZ0987654321	Unknown	XY	100	XY	T:C	0.1	0.1
+S02-A02	GS34251	T	C	XYZ0987654321	Unknown	XY	99	XY	T:C	0.1	0.1
+S02-A03	GS35220	C	T	XYZ0987654321	Unknown	XY	98	XY	C:T	0.1	0.1
+S02-A04	GS35220	C	T	XYZ0987654321	Unknown	XY	97	XY	C:T	0.1	0.1
+S02-A05	rs11096957	T	G	XYZ0987654321	Unknown	XY	100	No Call	No Call	0.1	0.1
+S02-A06	rs12828016	G	T	XYZ0987654321	Unknown	XY	100	No Call	No Call	0.1	0.1
+S02-A07	rs156697	A	G	XYZ0987654321	Unknown	XY	100	XY	A:G	0.1	0.1
+S02-A08	rs1801262	T	C	XYZ0987654321	Unknown	XY	100	XY	T:C	0.1	0.1
+S02-A09	rs1805034	C	T	XYZ0987654321	Unknown	XY	100	XY	C:T	0.1	0.1
+S02-A10	rs1805087	A	G	XYZ0987654321	Unknown	XY	100	XY	A:G	0.1	0.1
+S02-A11	rs2247870	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A12	rs2286963	T	G	XYZ0987654321	Unknown	XY	100	XY	T:G	0.1	0.1
+S02-A13	rs3742207	T	G	XYZ0987654321	Unknown	XY	100	XY	T:G	0.1	0.1
+S02-A14	rs3795677	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A15	rs4075254	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A16	rs4619	A	G	XYZ0987654321	Unknown	XY	100	XY	A:G	0.1	0.1
+S02-A17	rs4843075	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A18	rs5215	C	T	XYZ0987654321	Unknown	XY	100	XY	C:T	0.1	0.1
+S02-A19	rs6166	C	T	XYZ0987654321	Unknown	XY	100	XY	C:T	0.1	0.1
+S02-A20	rs649058	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A21	rs6557634	T	C	XYZ0987654321	Unknown	XY	100	XY	T:C	0.1	0.1
+S02-A22	rs6759892	T	G	XYZ0987654321	Unknown	XY	100	XY	T:G	0.1	0.1
+S02-A23	rs7298565	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A24	rs753381	T	C	XYZ0987654321	Unknown	XY	100	XY	T:C	0.1	0.1
+S02-A25	rs7627615	G	A	XYZ0987654321	Unknown	XY	100	XY	G:A	0.1	0.1
+S02-A26	rs8065080	T	C	XYZ0987654321	Unknown	XY	100	XY	T:C	0.1	0.1
+S02-A27				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A28				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A29				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A30				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A31				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A32				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A33				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
+S02-A34				[ Empty ]	NTC	NTC	100	NTC	NTC	0.1	0.1
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diff --git a/src/perl/t/fluidigm_qc/fluidigm_qc.csv b/src/perl/t/fluidigm_qc/fluidigm_qc.csv
new file mode 100644
index 000000000..add6dff97
--- /dev/null
+++ b/src/perl/t/fluidigm_qc/fluidigm_qc.csv
@@ -0,0 +1 @@
+ABC0123456789,1.0000,96,96,70,70,96,26,26,1381735059,S01,11413e77cde2a8dcca89705fe5b25a2d
diff --git a/src/perl/t/fluidigm_qc/fluidigm_qc_outdated_md5.csv b/src/perl/t/fluidigm_qc/fluidigm_qc_outdated_md5.csv
new file mode 100644
index 000000000..8302e6cf5
--- /dev/null
+++ b/src/perl/t/fluidigm_qc/fluidigm_qc_outdated_md5.csv
@@ -0,0 +1 @@
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