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Merge pull request #748 from wtsi-npg/devel
pull from devel to master to create release 96.0.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,36 @@ | ||
| #!/usr/bin/env perl | ||
| ######### | ||
| # Author: js10 | ||
| # Created: 2018-05-30 | ||
| # | ||
|
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| use strict; | ||
| use warnings; | ||
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| use FindBin qw($Bin); | ||
| use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" ); | ||
| use Carp; | ||
| use autodie qw(:all); | ||
| use Getopt::Long; | ||
| use Pod::Usage; | ||
|
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| use Monitor::Staging; | ||
| use Monitor::RunFolder::Staging; | ||
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| our $VERSION = '0'; | ||
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| use Readonly; | ||
| my $help; | ||
| my $runfolder_path; | ||
| my $status_update = 0; | ||
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| GetOptions ( | ||
| 'help' => \$help, | ||
| 'runfolder_path=s' => \$runfolder_path, | ||
| 'status_update!' => \$status_update, | ||
| ); | ||
| if ($help) { pod2usage(0); } | ||
|
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| if (!defined $runfolder_path || $runfolder_path == q[]) { | ||
| die "ERROR: --runfolder_path argument is required\n"; | ||
| } | ||
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| my @ms = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| status_update => $status_update | ||
| )->move_to_analysis(); | ||
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| my $mon = Monitor::RunFolder::Staging->new_with_options(status_update => 0); | ||
| my @ms = $mon->move_to_analysis(); | ||
| print join "\n", @ms; | ||
|
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| 1; | ||
|
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@@ -30,23 +40,38 @@ __END__ | |
| =head1 NAME | ||
| npg_move_runfolder - move 'incoming' to 'analysis' and change group. | ||
| npg_move_runfolder - move the run folder given as an argument from | ||
| 'incoming' to 'analysis' and change group. | ||
| =head1 VERSION | ||
| =head1 SYNOPSIS | ||
| C<npg_move_runfolder --runfolder_path path> | ||
| C<npg_move_runfolder --runfolder_path path> | ||
| =head1 DESCRIPTION | ||
| This script moves a given run folder from 'incoming' directory to 'analysis' directory | ||
| and changes the group name to that found in the staging configuration. | ||
| By default it does not change the run status. | ||
| This script moves a given run folder from 'incoming' directory to 'analysis' | ||
| directory and changes the group name to that found in the staging | ||
| configuration. By default it does not change the run status. | ||
| =head1 REQUIRED ARGUMENTS | ||
| C<runfolder_path> | ||
| =head1 OPTIONS | ||
| C<help> - displays help message and exists | ||
| C<runfolder_path> - the path of the run folder, required | ||
| C<status_update> - a boolean option, defaults to false, meaning that | ||
| the run status update is not performed | ||
| =head1 CONFIGURATION AND ENVIRONMENT | ||
| Depends on the presence of the npg tracking system. | ||
| If the run status update is performed, write access to the tracking | ||
| database is required. | ||
| =head1 INCOMPATIBILITIES | ||
|
|
@@ -58,7 +83,7 @@ Jennifer Liddle, E<lt>[email protected]<gt> | |
| =head1 LICENCE AND COPYRIGHT | ||
| Copyright (C) 2018 GRL, by Jennifer Liddle | ||
| Copyright (C) 2018, 2023 Genome Research Ltd. | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| #!/usr/bin/env perl | ||
|
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| use strict; | ||
| use warnings; | ||
| use FindBin qw($Bin); | ||
| use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" ); | ||
| use Log::Log4perl qw(:easy); | ||
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| use npg::samplesheet::auto; | ||
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| our $VERSION = '0'; | ||
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| Log::Log4perl->easy_init($INFO); | ||
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| my $log = Log::Log4perl->get_logger('main'); | ||
| $log->info('Starting npg samplesheet'); | ||
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| npg::samplesheet::auto->new()->loop(); | ||
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| 0; | ||
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| __END__ | ||
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| =head1 NAME | ||
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| npg_samplesheet4MiSeq | ||
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| =head1 USAGE | ||
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| npg_samplesheet4MiSeq | ||
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| =head1 DESCRIPTION | ||
|
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| The script, once started, runs in perpetuity, generating Illumina-style | ||
| samplesheets for any MiSeq run with status 'run pending'. | ||
|
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| =head1 REQUIRED ARGUMENTS | ||
|
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| None | ||
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| =head1 OPTIONS | ||
|
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| =head1 DIAGNOSTICS | ||
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| =head1 CONFIGURATION | ||
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| =head1 DEPENDENCIES | ||
|
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| =over | ||
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| =item strict | ||
|
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| =item warnings | ||
|
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| =item FindBin | ||
|
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| =item lib | ||
|
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| =item Log::Log4perl | ||
|
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| =item npg::samplesheet::auto | ||
|
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| =back | ||
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| =head1 EXIT STATUS | ||
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| Does not exit unless is sent a signal to terminate. | ||
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| =head1 INCOMPATIBILITIES | ||
|
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| =head1 BUGS AND LIMITATIONS | ||
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| =head1 AUTHOR | ||
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| Jaime Tovar E<lt>[email protected]<gt> | ||
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| =head1 LICENSE AND COPYRIGHT | ||
|
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| Copyright (C) 2020,2021,2023 GRL. | ||
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| This file is part of NPG. | ||
|
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| 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. | ||
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| 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. | ||
|
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| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
|
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| =cut |
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