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Commit a2733bff authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Embed module load cellranger into if/then/else

parent 2fb61286
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......@@ -71,15 +71,14 @@ process count {
file("**/outs/**") into outPaths
script:
"""
module load cellranger/2.1.1
"""
if (forceCells == 0){
"""
module load cellranger/2.1.1
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
"""
} else {
"""
module load cellranger/2.1.1
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
"""
}
......
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