Changes for release 1.14.1

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-- Script publish_infinium_file_list.pl; superseded by other publish scripts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-- Script publish_infinium_file_list.pl; superseded by other publish scripts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
 --------------------------
 

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