From 0d653b00e7698cf7e912864d7398a20b32884bce Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 18 Mar 2013 15:27:17 +0000
Subject: [PATCH] input ids are now templated on the flows not on the analysis
---
.../Pipeline/PipeConfig/FlatfileChecker_conf.pm | 8 +++-----
.../Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm | 12 +++++++-----
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm
index 7d92c09b72..36f4a48aab 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm
@@ -43,19 +43,17 @@ sub pipeline_analyses {
-parameters => {
inputcmd => 'find '.$self->o('base_path').q{ -type f -name '*.dat.gz'},
column_names => ['file'],
- randomize => 1,
- input_id_template => '{ file => "#file#" }'
+ randomize => 1
},
-input_ids => [ {} ],
-flow_into => {
- # 1 => 'Notify',
- 2 => ['CheckFlatfile'],
+ 2 => { CheckFlatfile => { file => '#file#'} }
},
},
{
-logic_name => 'CheckFlatfile',
-module => 'Bio::EnsEMBL::Pipeline::Flatfile::CheckFlatfile',
- -hive_capacity => 15,
+ -analysis_capacity => 15,
-rc_name => 'dump',
},
];
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm
index 3c6bc61515..000a931611 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm
@@ -70,17 +70,19 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Pipeline::Flatfile::DumpTypeFactory',
-parameters => {
types => $self->o('types'),
- input_id_template => '{ species => "#species#", type => "#type#" }',
- fan_branch_code => 2
},
- -flow_into => { 2 => ['DumpFlatfile', 'ChecksumGenerator'] },
+ -flow_into => {
+ 2 => { 'DumpFlatfile' => { species => "#species#", type => "#type#" },
+ 'ChecksumGenerator' => { species => "#species#", type => "#type#" },
+ },
+ },
},
{
-logic_name => 'DumpFlatfile',
-module => 'Bio::EnsEMBL::Pipeline::Flatfile::DumpFile',
-max_retry_count => 1,
- -hive_capacity => 10,
+ -analysis_capacity => 10,
-rc_name => 'dump',
},
@@ -90,7 +92,7 @@ sub pipeline_analyses {
-logic_name => 'ChecksumGenerator',
-module => 'Bio::EnsEMBL::Pipeline::Flatfile::ChecksumGenerator',
-wait_for => [qw/DumpFlatfile/],
- -hive_capacity => 10,
+ -analysis_capacity => 10,
},
####### NOTIFICATION
--
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