From 1d6236fd4307815385997965af2ebae3ac7aa392 Mon Sep 17 00:00:00 2001 From: puethe Date: Mon, 25 Nov 2019 17:51:17 +0000 Subject: [PATCH] do not request assembled/annotated=0 for velvet --- lib/Bio/VertRes/Config/Pipelines/AnnotateAssembly.pm | 11 +---------- .../Config/Recipes/BacteriaAssemblyAndAnnotation.pm | 2 +- .../Config/Recipes/BacteriaRegisterAndQCStudy.pm | 2 +- .../Config/Recipes/Roles/BacteriaRegisterStudy.pm | 1 - t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t | 3 +-- .../Config/Recipes/BacteriaAssemblyAndAnnotation.t | 4 +--- .../Config/Recipes/BacteriaRegisterAndQCStudy.t | 4 +--- 7 files changed, 6 insertions(+), 21 deletions(-) mode change 100644 => 100755 t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t diff --git a/lib/Bio/VertRes/Config/Pipelines/AnnotateAssembly.pm b/lib/Bio/VertRes/Config/Pipelines/AnnotateAssembly.pm index 979eb20..ea37d3e 100644 --- a/lib/Bio/VertRes/Config/Pipelines/AnnotateAssembly.pm +++ b/lib/Bio/VertRes/Config/Pipelines/AnnotateAssembly.pm @@ -55,16 +55,7 @@ override 'to_hash' => sub { $output_hash->{limit} = $self->_limit; $output_hash->{max_lanes_to_search} = $self->_max_lanes_to_search; $output_hash->{max_failures} = $self->_max_failures; - - if($self->_assembler eq 'velvet') - { - $output_hash->{vrtrack_processed_flags} = { assembled => 1, annotated => 0 }; - } - else - { - $output_hash->{vrtrack_processed_flags} = { assembled => 1}; - } - + $output_hash->{vrtrack_processed_flags} = { assembled => 1}; $output_hash->{limits} = $self->_escaped_limits; $output_hash->{data}{tmp_directory} = $self->_tmp_directory; diff --git a/lib/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.pm b/lib/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.pm index 0be555c..eae2986 100644 --- a/lib/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.pm +++ b/lib/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.pm @@ -24,7 +24,7 @@ has '_remove_primers' => ( is => 'ro', isa => 'Bool', default => 0 ); has '_pipeline_version' => ( is => 'ro', isa => 'Str' ); has '_normalise' => ( is => 'ro', isa => 'Bool', default => 0 ); has '_kingdom' => ( is => 'ro', isa => 'Str', default => "Bacteria" ); -has '_vrtrack_processed_flags' => ( is => 'ro', isa => 'HashRef', default => sub {{ assembled => 0, qc => 1, rna_seq_expression => 0 }} ); +has '_vrtrack_processed_flags' => ( is => 'ro', isa => 'HashRef', default => sub {{ qc => 1, rna_seq_expression => 0 }} ); has 'iva_qc' => ( is => 'ro', isa => 'Bool', default => 0 ); has 'kraken_db' => ( is => 'ro', isa => 'Str', default => "/lustre/scratch118/infgen/pathogen/pathpipe/kraken/assemblyqc_fluhiv_20150728" ); has 'spades_opts' => ( is => 'ro', isa => 'Str', default => ' --careful --cov-cutoff auto ' ); diff --git a/lib/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.pm b/lib/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.pm index b83d888..ab4db45 100644 --- a/lib/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.pm +++ b/lib/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.pm @@ -30,7 +30,7 @@ has '_remove_primers' => ( is => 'ro', isa => 'Bool', default => 0 ); has '_pipeline_version' => ( is => 'ro', isa => 'Str' ); has '_normalise' => ( is => 'ro', isa => 'Bool', default => 0 ); has '_kingdom' => ( is => 'ro', isa => 'Str', default => "Bacteria" ); -has '_vrtrack_processed_flags' => ( is => 'ro', isa => 'HashRef', default => sub {{ assembled => 0, qc => 1, rna_seq_expression => 0 }} ); +has '_vrtrack_processed_flags' => ( is => 'ro', isa => 'HashRef', default => sub {{ qc => 1, rna_seq_expression => 0 }} ); has 'iva_qc' => ( is => 'ro', isa => 'Bool', default => 0 ); has 'kraken_db' => ( is => 'ro', isa => 'Str', default => "/lustre/scratch118/infgen/pathogen/pathpipe/kraken/assemblyqc_fluhiv_20150728" ); has 'spades_opts' => ( is => 'ro', isa => 'Str', default => ' --careful --cov-cutoff auto ' ); diff --git a/lib/Bio/VertRes/Config/Recipes/Roles/BacteriaRegisterStudy.pm b/lib/Bio/VertRes/Config/Recipes/Roles/BacteriaRegisterStudy.pm index 03296c4..88e066e 100644 --- a/lib/Bio/VertRes/Config/Recipes/Roles/BacteriaRegisterStudy.pm +++ b/lib/Bio/VertRes/Config/Recipes/Roles/BacteriaRegisterStudy.pm @@ -78,7 +78,6 @@ sub add_bacteria_velvet_assembly_config _error_correct => $self->_error_correct, _remove_primers => $self->_remove_primers, _normalise => $self->_normalise, - _vrtrack_processed_flags => $self->_vrtrack_processed_flags, iva_qc => $self->iva_qc, kraken_db => $self->kraken_db, ) diff --git a/t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t b/t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t old mode 100644 new mode 100755 index 7b5c513..c9b0161 --- a/t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t +++ b/t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t @@ -61,8 +61,7 @@ is_deeply( }, 'max_lanes_to_search' => 10000, 'vrtrack_processed_flags' => { - 'assembled' => 1, - 'annotated' => 0 + 'assembled' => 1 }, 'root' => '/path/to/root/my_database/seq-pipelines', 'log' => '/path/to/log/my_database/annotate_assembly_Abc_def_ghi123_velvet.log', diff --git a/t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t b/t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t index 8effe24..b088e54 100755 --- a/t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t +++ b/t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t @@ -75,7 +75,6 @@ is_deeply($input_config_file,{ ] }, 'vrtrack_processed_flags' => { - 'assembled' => 0, 'rna_seq_expression' => 0, 'qc' => 1 }, @@ -127,8 +126,7 @@ is_deeply($input_config_file,{ ] }, 'vrtrack_processed_flags' => { - 'assembled' => 1, - 'annotated' => 0 + 'assembled' => 1 }, 'root' => '/lustre/scratch118/infgen/pathogen/pathpipe/my_database/seq-pipelines', 'log' => '/nfs/pathnfs05/log/my_database/annotate_assembly_ABC_study_EFG_velvet.log', diff --git a/t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t b/t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t index 743b706..d71f2b3 100755 --- a/t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t +++ b/t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t @@ -139,7 +139,6 @@ is_deeply($input_config_file,{ ] }, 'vrtrack_processed_flags' => { - 'assembled' => 0, 'rna_seq_expression' => 0, 'qc' => 1 }, @@ -191,8 +190,7 @@ is_deeply($input_config_file,{ ] }, 'vrtrack_processed_flags' => { - 'assembled' => 1, - 'annotated' => 0 + 'assembled' => 1 }, 'root' => '/lustre/scratch118/infgen/pathogen/pathpipe/my_database/seq-pipelines', 'log' => '/nfs/pathnfs05/log/my_database/annotate_assembly_ABC_study_EFG_velvet.log',