From 347873e05b2341e9a00904e9c59ffb6e0a06fc82 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Thu, 18 Apr 2019 22:29:10 +0200
Subject: [PATCH] add reporting
---
main.nf | 49 +++++++++++++++++++++++++++----------------------
1 file changed, 27 insertions(+), 22 deletions(-)
diff --git a/main.nf b/main.nf
index 60fe35c..5550fb1 100644
--- a/main.nf
+++ b/main.nf
@@ -249,31 +249,36 @@ log.info """=======================================================
nf-core/hic v${workflow.manifest.version}"
======================================================="""
def summary = [:]
-summary['Pipeline Name'] = 'nf-core/hic'
+summary['Pipeline Name'] = 'nf-core/hic'
summary['Pipeline Version'] = workflow.manifest.version
-summary['Run Name'] = custom_runName ?: workflow.runName
-
-summary['Reads'] = params.reads
-summary['Fasta Ref'] = params.fasta
-
-
-summary['Max Memory'] = params.max_memory
-summary['Max CPUs'] = params.max_cpus
-summary['Max Time'] = params.max_time
-summary['Output dir'] = params.outdir
-summary['Working dir'] = workflow.workDir
+summary['Run Name'] = custom_runName ?: workflow.runName
+
+summary['Reads'] = params.reads
+summary['splitFastq'] = params.splitFastq
+summary['Fasta Ref'] = params.fasta
+summary['Ligation Motif'] = params.ligation_site
+summary['DNase Mode'] = params.dnase
+summary['Remove Dup'] = params.rm_dup
+summary['Maps resolution'] = params.bin_size
+
+summary['Max Memory'] = params.max_memory
+summary['Max CPUs'] = params.max_cpus
+summary['Max Time'] = params.max_time
+summary['Output dir'] = params.outdir
+summary['Working dir'] = workflow.workDir
summary['Container Engine'] = workflow.containerEngine
-if(workflow.containerEngine) summary['Container'] = workflow.container
-summary['Current home'] = "$HOME"
-summary['Current user'] = "$USER"
-summary['Current path'] = "$PWD"
-summary['Working dir'] = workflow.workDir
-summary['Output dir'] = params.outdir
-summary['Script dir'] = workflow.projectDir
-summary['Config Profile'] = workflow.profile
+if(workflow.containerEngine)
+ summary['Container'] = workflow.container
+summary['Current home'] = "$HOME"
+summary['Current user'] = "$USER"
+summary['Current path'] = "$PWD"
+summary['Working dir'] = workflow.workDir
+summary['Output dir'] = params.outdir
+summary['Script dir'] = workflow.projectDir
+summary['Config Profile'] = workflow.profile
if(workflow.profile == 'awsbatch'){
- summary['AWS Region'] = params.awsregion
- summary['AWS Queue'] = params.awsqueue
+ summary['AWS Region'] = params.awsregion
+ summary['AWS Queue'] = params.awsqueue
}
if(params.email) summary['E-mail Address'] = params.email
log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
--
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