diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml index abc57729d489c424fed514a9f0cafad382a557a3..dfd401565433a69cc1ede56aa7bdd9fc7aff46d1 100755 --- a/astrocyte_pkg.yml +++ b/astrocyte_pkg.yml @@ -120,7 +120,7 @@ workflow_parameters: max: 10000 required: false description: | - Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. + Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells. # ----------------------------------------------------------------------------- # SHINY APP CONFIGURATION diff --git a/workflow/main.nf b/workflow/main.nf index dbd69e8f76d13fa6f82deb0126b755860e3f746c..a0bcf3f74e2d88710063f6808df98f9418464d98 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -81,13 +81,13 @@ process count { """ module load cellranger/2.1.1 """ - if ( forceCells ==0){ + if (forceCells == 0){ """ cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells """ } else { """ - cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells --force-cells=$forceCells + cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells """ } -} \ No newline at end of file +}