From 2d5e45602a2ea7979520f301ef964c46b8a3261f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 28 Jun 2019 11:48:38 -0500
Subject: [PATCH] Make seetings match mkfastq

---
 workflow/conf/biohpc.config |  8 ++++++++
 workflow/main.nf            | 29 +++++++++++++++++------------
 2 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 6f19408..6e35646 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -18,6 +18,14 @@ process {
     module = ['cellranger/3.0.2']
     queue = '128GB,256GB,256GBv1,384GB'
   }
+  withLabel: versions {
+    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+    executor = 'local'
+  }
+  withLabel: multiqc {
+    module = ['multiqc/1.7']
+    executor = 'local'
+  }
 }
 
 params {
diff --git a/workflow/main.nf b/workflow/main.nf
index 6006190..a968f58 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -14,7 +14,7 @@ params.kitVersion = 'three'
 params.version = '3.0.2'
 params.astrocyte = false
 params.outDir = "$baseDir/output"
-params.multiqc = "$baseDir/conf/multiqc_config.yaml"
+params.multiqcConf = "$baseDir/conf/multiqc_config.yaml"
 params.references = "$baseDir/../docs/references.md"
 
 // Assign variables if astrocyte
@@ -56,11 +56,11 @@ forceCells = params.forceCells
 chemistryParam = params.chemistryParam
 version = params.version
 outDir = params.outDir
-multiqc = params.multiqc
+multiqcConf = params.multiqc
 references = params.references
 
-process checkDesignFile {
 
+process checkDesignFile {
   publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
   module 'python/3.6.1-2-anaconda'
 
@@ -82,6 +82,7 @@ process checkDesignFile {
   """
 }
 
+
 // Parse design file
 samples = designPaths
   .splitCsv (sep: ',', header: true)
@@ -109,6 +110,7 @@ forceCells302 = forceCells
 chemistryParam301 = chemistryParam
 chemistryParam302 = chemistryParam
 
+
 process count211 {
   queue '128GB,256GB,256GBv1,384GB'
   tag "$sample"
@@ -125,7 +127,7 @@ process count211 {
   output:
 
   file("**/outs/**") into outPaths211
-  file("*_metrics_summary.tsv") into metricsSummary211
+  file("*_metrics_summary.tsv") into metricsSummary
 
   when:
   version == '2.1.1'
@@ -150,6 +152,7 @@ process count211 {
   }
 }
 
+
 process count301 {
   queue '128GB,256GB,256GBv1,384GB'
   tag "$sample"
@@ -167,7 +170,7 @@ process count301 {
   output:
 
   file("**/outs/**") into outPaths301
-  file("*_metrics_summary.tsv") into metricsSummary301
+  file("*_metrics_summary.tsv") into metricsSummary
 
   when:
   version == '3.0.1'
@@ -192,6 +195,7 @@ process count301 {
   }
 }
 
+
 process count302 {
   queue '128GB,256GB,256GBv1,384GB'
   tag "$sample"
@@ -209,7 +213,7 @@ process count302 {
   output:
 
   file("**/outs/**") into outPaths302
-  file("*_metrics_summary.tsv") into metricsSummary302
+  file("*_metrics_summary.tsv") into metricsSummary
 
   when:
   version == '3.0.2'
@@ -237,7 +241,7 @@ process count302 {
 
 process versions {
   tag "$name"
-  publishDir "$outDir/${task.process}", mode: 'copy'
+  publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
   module 'python/3.6.1-2-anaconda:pandoc/2.7:multiqc/1.7'
 
   input:
@@ -259,11 +263,11 @@ process versions {
   """
 }
 
-metricsSummary = metricsSummary211.mix(metricsSummary301, metricsSummary302)
 
 // Generate MultiQC Report
-process multiqcReport {
+process multiqc {
   publishDir "$outDir/${task.process}", mode: 'copy'
+  module 'multiqc/1.7'
 
   input:
 
@@ -272,14 +276,15 @@ process multiqcReport {
 
   output:
 
-  file "multiqc_report.html" into multiqcReport
+  file "*" into mqcPaths
 
   script:
 
   """
+  hostname
+  ulimit -a
   awk 'FNR==1 && NR!=1{next;}{print}' *.tsv > metrics_summary_mqc.tsv
   sed -i '1s/^.*\tE/Sample\tE/' metrics_summary_mqc.tsv
-  module load multiqc/1.7
-  multiqc -c $multiqc .
+  multiqc -c $multiqcConf
   """
 }
-- 
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