Merge branch 'develop' into 'master'

Fix multi sample, local ulimit set, v2.1.1

See merge request !74

CHANGELOG.md

-# v2.1.0
+# v2.1.1
 **User Facing**
 * Check Design File for spaces in name and file contents
 * Attempt to prevent thredding error (which appears to only happen on 256GBv1 nodes)

workflow/main.nf

@@ -33,7 +33,7 @@ params.outDir = "${baseDir}/output"
 // Variable error test
 if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
   print("Cellranger Version 2.1.1 requires kitVersion 2")
-  System.exit(32)	
+  System.exit(1)	
 }
 
 // Define variables if astrocyte (or from config)
@@ -60,7 +60,7 @@ if (params.astrocyte) {
 params.genomeLocationFull = params.genomeLocation+params.genome
 
 // Define variables from input
-pipelineVersion = "2.1.0"
+pipelineVersion = "2.1.1"
 name = params.name
 designLocation = Channel
   .fromPath(params.designFile)
@@ -99,7 +99,6 @@ process trackStart {
   script:
   """
   hostname
-  ulimit -u 16384
   ulimit -a
   export https_proxy=\${http_proxy}
  
@@ -135,7 +134,6 @@ process checkDesignFile {
   script:
     """
     hostname
-    ulimit -u 16384
     ulimit -a
     noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
     if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
@@ -151,9 +149,11 @@ samples = designPaths
   .splitCsv (sep: ',', header: true)
   .map { row -> [ row.Sample, file(row.fastq_R1), file(row.fastq_R2) ] }
   .groupTuple()
+  .combine(filename_checkScript)
   //.subscribe { println it }
 
 // Duplicate variables
+
 samples.into {
   samples211
   samples302
@@ -173,11 +173,6 @@ forceCells310 = forceCells
 chemistryParam211 = chemistryParam
 chemistryParam302 = chemistryParam
 chemistryParam310 = chemistryParam
-filename_checkScript.into {
-  filename_checkScript211
-  filename_checkScript302
-  filename_checkScript310
-}
 
 
 /*
@@ -190,12 +185,11 @@ process count211 {
   module 'cellranger/2.1.1'
 
   input:
-    set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples211
+    set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples211
     file ref from refLocation211.first()
     expectCells211
     forceCells211
     chemistryParam211
-    file filename_checkScript211
 
   output:
     file("**/outs/**") into outPaths211
@@ -238,12 +232,11 @@ process count302 {
   module 'cellranger/3.0.2'
 
   input:
-    set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples302
+    set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples302
     file ref from refLocation302.first()
     expectCells302
     forceCells302
     chemistryParam302
-    file filename_checkScript302
 
   output:
     file("**/outs/**") into outPaths302
@@ -285,12 +278,11 @@ process count310 {
   module 'cellranger/3.1.0'
 
   input:
-    set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples310
+    set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples310
     file ref from refLocation310.first()
     expectCells310
     forceCells310
     chemistryParam310
-    file filename_checkScript310
 
   output:
     file("**/outs/**") into outPaths310
@@ -340,7 +332,6 @@ process versions {
   script:
     """
     hostname
-    ulimit -u 16384
     ulimit -a
     echo "${workflow.nextflow.version}" > version_nextflow.txt
     echo "${pipelineVersion}" > version_pipeline.txt
@@ -372,7 +363,6 @@ process multiqc {
   script:
     """
     hostname
-    ulimit -u 16384
     ulimit -a
     awk 'FNR==1 && NR!=1{next;}{print}' *.tsv > metrics_summary_mqc.tsv
     sed -i '1s/^.*\tE/Sample\tE/' metrics_summary_mqc.tsv

workflow/nextflow.config

@@ -47,6 +47,6 @@ manifest {
   homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
   description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
   mainScript = 'main.nf'
-  version = '2.1.0'
+  version = '2.1.1'
   nextflowVersion = '>=0.31.0'
 }