Transcript assembly and quantification for RNA-Se
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, strandedness:‘forward’ ]
srbam
:file
Sorted and indexed bam file from short-read alignment.
.bam
lrbam
Sorted and indexed bam file from long-read alignment.
mode
:string
StringTie mode (long-read-assembly, mix-read-assembly, expression-estimation, nascent-aware-assembly).
annotation_gtf
Annotation gtf file (optional).
.gtf
transcript_gtf
${prefix}.transcripts.gtf
Output assembly (transcriptome)
abundance
${prefix}.gene.abundance.txt
Abundance for non-redundand set of transcripts
.txt
coverage_gtf
${prefix}.coverage.gtf
Coverage for the sample
ballgown
${prefix}.ballgown/*.ctab
Ballgown output for the sample
.ctab
versions_stringtie
${task.process}
The name of the process
stringtie
The name of the tool
stringtie --version
:eval
The expression to obtain the version of the tool
versions
Transcript assembly and quantification for RNA-Seq
