update with singularity

nextflow.config

@@ -6,22 +6,25 @@ process {
   clusterOptions = '--hold --no-kill'
   queue = '128GB,256GB,256GBv1'
   withLabel: trim {
-    container = 'goalconsortium/trim_galore:1.0.4'
+    container = 'trim_galore.sif'
   }
   withLabel: dnaalign {
-     container = 'goalconsortium/dna_alignment:1.0.4'
+     container = 'dna_alignment.sif'
   }
   withLabel: profiling_qc {
-    container = 'goalconsortium/profiling_qc:1.0.4'
+    container = 'profiling_qc.sif'
   }
-  withName: starfusion {
-    container = 'goalconsortium/starfusion:1.0.4'
+  withLabel: starfusion {
+    container = 'starfusion.sif'
   }
-  withName: ralign {
-    container = 'goalconsortium/rna_alignment:1.0.4'
+  withLabel: ralign {
+    container = 'rna_alignment.sif'
   }
-  withName: geneabund {
-    container = 'goalconsortium/rna_gene_abundance:1.0.4'
+  withLabel: geneabund {
+    container = 'rna_gene_abundance.sif'
+  }
+  withLabel: rnaseqstat {
+    container = 'rnaseq_dea.sif'
   }
 }
 

workflow/main.nf

@@ -34,23 +34,18 @@ index_path = file(params.genome)
 
 process checkdesignfile {
 	queue 'super'
-	module 'parallel/20150122:pigz/2.4'
+	label 'trim'
 	publishDir "$params.output", mode: 'copy'
-
 	input:
         file design_file name 'design.ori.txt'
 	file ("*") from fqs.collect()
-
 	output:
 	file("design.valid.txt") into newdesign
 	file("*.fastq.gz") into fastqs mode flatten
 	stdout spltnames
-
 	script:
 	"""
-	bash $baseDir/scripts/check_inputfiles.sh 
-	perl -p -e 's/\\r\\n*/\\n/g' design.ori.txt > design.fix.txt
-	perl $baseDir/scripts/check_designfile.pl ${params.pairs} design.fix.txt
+	bash $repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
 	"""
 }
 
@@ -159,6 +154,7 @@ process geneabund {
 process statanal {
   errorStrategy 'ignore'
   publishDir "$params.output", mode: 'copy'
+  label 'rnaseqstat'
   input:
   file count_file from counts.toList()
   file count_sum from ctsum.toList()

process_scripts @ 8706de70

-Subproject commit 96bcf78802267e8bb1834c06ffb98c5d700273e3
+Subproject commit 8706de703b8b5933f89651e5be0312af96cddb7c