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Code suggestions #140

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merged 3 commits into from
Sep 15, 2023
Merged

Code suggestions #140

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123e1bc
This should work
muffato Sep 15, 2023
598de78
More straightforward variable name
muffato Sep 15, 2023
e9dd94d
Update TreeValProject.groovy
DLBPointon Sep 15, 2023
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9 changes: 7 additions & 2 deletions lib/TreeValProject.groovy
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
import java.time.OffsetDateTime;
import java.time.Duration;

class TreeValProject {
//
// Generates a small summary containing context for the input files
Expand All @@ -7,13 +10,15 @@ class TreeValProject {

public static void summary(workflow, params, metrics, log) {

def date_completed = OffsetDateTime.now()

def input_data = [:]
input_data['version'] = NfcoreTemplate.version( workflow )
input_data['runName'] = workflow.runName
input_data['session_id'] = workflow.sessionId
input_data['duration'] = 'CANNOT BE CALCULATED'
input_data['duration'] = Duration.between( workflow.start, date_completed ).toSeconds()
input_data['DateStarted'] = workflow.start
input_data['DateCompleted'] = new Date().format("yyyy-MM-dd HH:mm:ss.SSSZ")
input_data['DateCompleted'] = date_completed
input_data['entry'] = params.entry

input_data['input_yaml'] = params.input
Expand Down
8 changes: 4 additions & 4 deletions subworkflows/local/hic_mapping.nf
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Expand Up @@ -154,12 +154,12 @@ workflow HIC_MAPPING {
// LOGIC: HIRES IS TOO INTENSIVE FOR RUNNING IN GITHUB CI SO THIS STOPS IT RUNNING
//
if ( params.config_profile_name ) {
github = params.config_profile_name
config_profile_name = params.config_profile_name
} else {
github = 'Local'
config_profile_name = 'Local'
}

if ( !github.contains('GitHub') ) {
if ( !config_profile_name.contains('GitHub') ) {
//
// MODULE: GENERATE PRETEXT MAP FROM MAPPED BAM FOR HIGH RES
//
Expand Down Expand Up @@ -211,7 +211,7 @@ workflow HIC_MAPPING {
//
// LOGIC: SECTION ONLY NEEDED FOR TREEVAL VISUALISATION, NOT RAPID ANALYSIS
//
if (workflow_setting == 'FULL' && !github.contains('GitHub')) {
if (workflow_setting == 'FULL' && !config_profile_name.contains('GitHub')) {
//
// LOGIC: PREPARE JUICER TOOLS INPUT
//
Expand Down