Nextflow Registry | nf-core/rsem/calculateexpression@0.0.0-6c4ed3a

nf-core/rsem/calculateexpression @ 0.0.0-6c4ed3a

Calculate expression with RSEM

rsem expression quantification

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @drpatelh @kevinmenden

Maintainers: @drpatelh @kevinmenden

Calculate expression with RSEM

Add the following snippet to your workflow script to include this module.

include { RSEM_CALCULATEEXPRESSION } from 'nf-core/rsem/calculateexpression'

MIT License

Process

`Name`	`RSEM_CALCULATEEXPRESSION`

Input 2 channels

#1 tuple

`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` file	RSEM index `rsem/*`

Output 9 channels

#1 logs tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	RSEM logs `*.log`

#2 stat tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.stat` file	RSEM statistics `*.stat`

#3 bam_star tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.STAR.genome.bam` file	BAM file generated by STAR (optional) `*.STAR.genome.bam`

#4 bam_genome tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}.genome.bam` file	Genome BAM file (optional) `*.genome.bam`

#5 counts_gene tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.genes.results` file	Expression counts on gene level `*.genes.results`

#6 versions_rsem tuple

`${task.process}` string	The name of the process
`rsem` string	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

#7 versions_star tuple

`${task.process}` string	The name of the process
`star` string	The name of the tool
`STAR --version \| sed -e "s/STAR_//g"` eval	The expression to obtain the version of the tool

#8 bam_transcript tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}.transcript.bam` file	Transcript BAM file (optional) `*.transcript.bam`

#9 counts_transcript tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.isoforms.results` file	Expression counts on transcript level `*.isoforms.results`

Tool	Description	Homepage
rseqc	RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome	https://github.com/deweylab/RSEM

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b