Calculate expression with RSEM
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
Input reads for quantification (FASTQ files or BAM file for —alignments mode)
*.{fastq.gz,bam}
index
RSEM index
rsem/*
counts_gene
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*.genes.results
Expression counts on gene level
counts_transcript
*.isoforms.results
Expression counts on transcript level
stat
*.stat
RSEM statistics
logs
*.log
RSEM logs
versions_rsem
${task.process}
:string
The name of the process
rsem
The name of the tool
rsem-calculate-expression --version | sed 's/Current version: RSEM v//'
:eval
The expression to obtain the version of the tool
versions_star
star
STAR --version | sed -e "s/STAR_//g"
bam_star
*.STAR.genome.bam
BAM file generated by STAR (optional)
bam_genome
${prefix}.genome.bam
Genome BAM file (optional)
*.genome.bam
bam_transcript
${prefix}.transcript.bam
Transcript BAM file (optional)
*.transcript.bam
versions
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
