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PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors

• Close issue
  Closes #

/cc @ghenry

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}