1.0 10xGenomics data demo Demo of Eoulsan for 10xGenomics data (single-cell RNA seq) Lehmann starindexgenerator overhang 100 use.gtf.file true gtf.feature.exon exon gtf.tag.exon.parent.transcript Parent fastqc filterreads illuminaid quality.threshold 30 fastqc umiwhitelist umiextract mapreads mapper star mapper.arguments --outSAMunmapped Within filtersam removeunmapped true removemultimatches true featurecounts input step8filtersam output multiqc reports fastqc,mapreads,featurecounts use.docker true sam2bam input step9featurecounts outputsam umicount rsinglecellexperimentcreator input.matrices true design.prefix Cell. r.execution.mode docker main.docker.uri unix:///var/run/docker.sock