Merge pull request #578 from wtsi-npg/devel

merge devel into master to create release 91.4.0

Changes

@@ -1,5 +1,12 @@
 LIST OF CHANGES
 
+release 91.4.0
+ - disable downloading *.fa (consensus) files from tracking server
+   views of staging folders
+ - add executable for npg samplesheet4MiSeq wrapper
+ - st::api::lims - two new accessors, 'sample_is_control'
+   and 'sample_control_type'
+
 release 91.3.0
  - pp_archive_path runfolder accessor - a path to an archive directory
    for third party portable pipelines

MANIFEST

@@ -2,6 +2,7 @@ bin/event_notifications
 bin/illumina_instruments_uptime
 bin/npg_daemon_control
 bin/npg_move_runfolder
+bin/npg_samplesheet4MiSeq
 bin/npg_status2file
 bin/npg_status_watcher
 bin/staging_area_monitor

bin/npg_samplesheet4MiSeq

@@ -0,0 +1,92 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" );
+use Log::Log4perl qw(:easy);
+
+use npg::samplesheet::auto;
+
+our $VERSION = '0';
+
+Log::Log4perl->easy_init($INFO);
+
+my $log = Log::Log4perl->get_logger('main');
+$log->info("Starting npg samplesheet");
+
+npg::samplesheet::auto->new()->loop();
+
+exit 0;
+
+1;
+
+__END__
+
+=head1 NAME
+
+npg_samplesheet4MiSeq
+
+=head1 USAGE
+
+  npg_samplesheet4MiSeq
+
+=head1 DESCRIPTION
+
+  The script, once started, runs in perpetuity, generating Illumina-style
+  samplesheets for any MiSeq run with status 'run pending'.
+
+=head1 REQUIRED ARGUMENTS
+
+  None
+
+=head1 OPTIONS
+
+=head1 DIAGNOSTICS
+
+=head1 CONFIGURATION
+
+=head1 DEPENDENCIES
+
+=over
+
+=item strict
+
+=item warnings
+
+=item FindBin
+
+=item lib
+
+=item Log::Log4perl
+
+=back
+
+=head1 INCOMPATIBILITIES
+
+=head1 BUGS AND LIMITATIONS
+
+=head1 AUTHOR
+
+Jaime Tovar E<lt>[email protected]<gt>
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright (C) 2020 Genome Research Limited
+
+This file is part of NPG.
+
+NPG is free software: you can redistribute it and/or modify
+it under the terms of 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.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+=cut

lib/st/api/lims.pm

@@ -111,6 +111,8 @@ Readonly::Hash   my  %METHODS_PER_CATEGORY => {
                            sample_supplier_name
                            sample_cohort
                            sample_donor_id
+                           sample_is_control
+                           sample_control_type
                       /],
 
     'study'        => [qw/ study_id

t/40-st-lims-mlwarehouse.t

@@ -8,7 +8,7 @@ my $available = eval "require $driver_package";
 if (!$available) {
   plan skip_all => "$driver_package is not deployed or cannot be loaded";
 } else {
-  plan tests => 5;
+  plan tests => 6;
 
   use_ok('st::api::lims');
 
@@ -144,6 +144,25 @@ if (!$available) {
 
   };
 
+  subtest 'sample controls' => sub {
+    plan tests => 6;
+
+    my $init = {id_flowcell_lims => 57543, position => 1,
+                driver_type => 'ml_warehouse', mlwh_schema => $schema_wh};
+
+    for my $ti ((1,2,3)) {
+      $init->{tag_index} = $ti;
+      my $l = st::api::lims->new($init);
+      if ($ti <= 2 ) {
+        ok($l->sample_is_control, 'sample is control');
+        my $ctype = ($ti == 1) ? 'negative' : 'positive';
+        is($l->sample_control_type, $ctype, 'correct control type');
+      } else {
+        ok(!$l->sample_is_control, 'sample is not control');
+        is($l->sample_control_type, undef, 'sample control type is undefined');
+      }
+    }
+  };
 }
 
 1;

t/40-st-lims.t

@@ -5,7 +5,7 @@ use Test::Exception;
 use Test::Warn;
 use File::Temp qw/ tempdir /;
 
-my $num_delegated_methods = 46;
+my $num_delegated_methods = 48;
 
 local $ENV{'http_proxy'} = 'http://wibble.com';
 
@@ -433,7 +433,7 @@ subtest 'Object for a tag' => sub {
 };
 
 subtest 'Object for a non-pool lane' => sub {
-  plan tests => 97;
+  plan tests => 99;
 
   my $lims = st::api::lims->new(id_run => 6607, position => 1);
   isa_ok($lims, 'st::api::lims');

t/data/fixtures_lims_wh/000-Sample.yml

@@ -462,7 +462,8 @@
   cohort: ~
   common_name: ~
   consent_withdrawn: 0
-  control: ~
+  control: 1
+  control_type: negative
   country_of_origin: ~
   created: 2017-10-19 13:30:14
   deleted_at: ~
@@ -492,7 +493,8 @@
   cohort: ~
   common_name: ~
   consent_withdrawn: 0
-  control: ~
+  control: 1
+  control_type: positive
   country_of_origin: ~
   created: 2017-10-19 13:30:14
   deleted_at: ~

t/data/samplesheet/1control7libs_extended.csv

@@ -1,10 +1,10 @@
-[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Lane,Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_description,sample_donor_id,sample_id,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index,
-1,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36189,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
-2,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36199,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
-3,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36202,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
-4,79577,phiX CT1462-2 1,,,,,,,,,,,1,0,,,phiX CT1462-2 1,,,,,,standard,,43779,,,,,,,,9836,phiX CT1462-2 1,,,,,,,0,0,,,,,,,,
-5,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36203,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
-6,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36209,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
-7,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36210,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
-8,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36211,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,7283,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Lane,Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index,
+1,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36189,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+2,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36199,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+3,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36202,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+4,79577,phiX CT1462-2 1,,,,,,,,,,,1,0,,,phiX CT1462-2 1,,,,,,standard,,43779,,,,,,,,,9836,,phiX CT1462-2 1,,,,,,,0,0,,,,,,,,
+5,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36203,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+6,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36209,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+7,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36210,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,
+8,57440,EGAN00001001569,,,,,,[email protected] [email protected] [email protected] [email protected],[email protected] [email protected] [email protected],[email protected],[email protected],,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36211,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from  total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,,