Merge branch '44-fix.tread.error' into 'develop'

Add ulimit -u to all cellranger processes

Closes #44

See merge request !66

workflow/main.nf

@@ -164,6 +164,7 @@ process count211 {
     if (forceCells211 == 0) {
       """
       hostname
+      ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211} --chemistry=${chemistryParam211}
@@ -173,6 +174,7 @@ process count211 {
     else {
       """
       hostname
+      ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211} --chemistry=${chemistryParam211}
@@ -208,6 +210,7 @@ process count220 {
     if (forceCells220 == 0) {
       """
       hostname
+      ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells220} --chemistry=${chemistryParam220}
@@ -217,6 +220,7 @@ process count220 {
     else {
       """
       hostname
+      ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells220} --chemistry=${chemistryParam220}
@@ -298,6 +302,7 @@ process count310 {
     if (forceCells310 == 0) {
       """
       hostname
+      ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells310} --chemistry=${chemistryParam310}