diff --git a/workflow/main.nf b/workflow/main.nf index c12e30ddae4592bf28c80ea772e1f3bdb9fdb9d4..ec068ca61a42f82f99c9587c48e64e75ae89f0a1 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -71,6 +71,8 @@ process checkDesignFile { script: """ + hostname + ulimit -a module load python/3.6.1-2-anaconda python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList """ @@ -129,10 +131,14 @@ process count211 { """ if (forceCells211 == 0){ """ + hostname + ulimit -a cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211 """ } else { """ + hostname + ulimit -a cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211 """ } @@ -165,10 +171,14 @@ process count301 { """ if (forceCells301 == 0){ """ + hostname + ulimit -a cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301" """ } else { """ + hostname + ulimit -a cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301" """ } @@ -201,10 +211,14 @@ process count302 { """ if (forceCells302 == 0){ """ + hostname + ulimit -a cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302" """ } else { """ + hostname + ulimit -a cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302" """ }