removed Skip_WF map_headers_to_tab command as default p_func config s…

…etting. Will prematurely exit script if genecalls pipeline is run.
jorvis · Jul 27, 2015 · b34afb5 · b34afb5
1 parent a0120fb
commit b34afb5
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Showing 4 changed files with 9 additions and 3 deletions.
diff --git a/components/p_func/p_func.config b/components/p_func/p_func.config
@@ -41,7 +41,7 @@ $;COMPONENT_NAME$; = p_func
 $;DESCRIPTION$; = none
 $;WORKFLOW_REPOSITORY$; = $;REPOSITORY_ROOT$;/workflow/runtime/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
 $;PIPELINE_TOKEN$; = unnamed
-$;SKIP_WF_COMMAND$;=map headers to tab
+$;SKIP_WF_COMMAND$;=
 
 ;The version,revision,tag here is set by an interpolated CVS tag
 $;VERSION$; = 2.0

diff --git a/src/perl/map_header_to_transcript_in_tab.pl b/src/perl/map_header_to_transcript_in_tab.pl
@@ -229,6 +229,13 @@ sub check_options {
 
    $debug = $opts->{'debug'} if( $opts->{'debug'} );
 
+   # If feature_relationhip file is not present, then we assume mapping does not need to take place
+   if (! $opts->{'feature_relationship_file'}){
+		print STDERR "No feature_relationship file found so skipping rest of mapping program.\n";
+		exit(0);
+	}
+
+
    foreach my $req ( qw(tabfile feature_relationship_file pseudomolecule_list output_file) ) {
        &_log($ERROR, "Option $req is required") unless( $opts->{$req} );
    }

diff --git a/templates/pipelines/Prokaryotic_Annotation_Pipeline_Gene_Annotations/p_func.default.config b/templates/pipelines/Prokaryotic_Annotation_Pipeline_Gene_Annotations/p_func.default.config
@@ -41,7 +41,7 @@ $;COMPONENT_NAME$; = p_func
 $;DESCRIPTION$; = none
 $;WORKFLOW_REPOSITORY$; = $;REPOSITORY_ROOT$;/workflow/runtime/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
 $;PIPELINE_TOKEN$; = unnamed
-$;SKIP_WF_COMMAND$;=map headers to tab
+$;SKIP_WF_COMMAND$;=
 
 ;The version,revision,tag here is set by an interpolated CVS tag
 $;VERSION$; = 2.0

diff --git a/util/create_prok_pipeline_config.pl b/util/create_prok_pipeline_config.pl
@@ -322,7 +322,6 @@ =head1  CONTACT
 	$config{'overlap_analysis default'}->{'$;RNA_BSML$;'} = '';
 	$config{'pipeline_summary default'}->{'$;OTHER_BSML_LISTS$;'} = '';
 
-	$config{'p_func default'}->{'$;SKIP_WF_COMMAND$;'} = '';
 	$config{'p_func default'}->{'$;FEATURE_RELATIONSHIP_FILE$;'} = '$;REPOSITORY_ROOT$;/output_repository/'.
 		'bsml2featurerelationships/$;PIPELINEID$;_pre_overlap_analysis/bsml2featurerelationships.mapping.list';
 	$config{'p_func default'}->{'$;PSEUDOMOLECULE_FILE$;'} = '$;REPOSITORY_ROOT$;/output_repository/create_pseudomolecules/$;PIPELINEID$;_genecalls/create_pseudomolecules.list';