Nextflow Registry | nf-core/sentieon/rsemcalculateexpression@0.0.0-6c4ed3a

nf-core/sentieon/rsemcalculateexpression @ 0.0.0-6c4ed3a

Calculate expression with RSEM

rsem expression quantification sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen

Calculate expression with RSEM

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

include { SENTIEON_RSEMCALCULATEEXPRESSION } from 'nf-core/sentieon/rsemcalculateexpression'

MIT License

Process

`Name`	`SENTIEON_RSEMCALCULATEEXPRESSION`

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.gz`

`index` file	RSEM index `rsem/*`

Output 10 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 process the versions were collected from
`rsem` string	The tool name
`rsem-calculate-expression --version \| sed -e "s/Current version: RSEM v//g"` eval	The expression to obtain the version of the tool

#7 versions_star tuple

`${task.process}` string	The process the versions were collected from
`star` string	The tool name
`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`

#10 versions_sentieon tuple

`sentieon driver --version 2>&1`
`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name