nf-core_modules/modules/rsem/calculateexpression/meta.yml

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name: rsem_calculateexpression
description: Calculate expression with RSEM
keywords:
- rsem
- expression
- quantification
tools:
- rseqc:
description: |
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
homepage: https://github.com/deweylab/RSEM
documentation: https://github.com/deweylab/RSEM
doi: https://doi.org/10.1186/1471-2105-12-323
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: Input reads for quantification
pattern: "*.fastq.gz"#
- index:
type: file
description: RSEM index
pattern: "rsem/*"
output:
- counts_gene:
type: file
description: Expression counts on gene level
pattern: "*.genes.results"
- counts_transctips:
type: file
description: Expression counts on transcript level
pattern: "*.isoforms.results"
- stat:
type: file
description: RSEM statistics
pattern: "*.stat"
- logs:
type: file
description: RSEM logs
pattern: "*.log"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam_star:
type: file
description: BAM file generated by STAR (optional)
pattern: "*.STAR.genome.bam"
- bam_genome:
type: file
description: Genome BAM file (optional)
pattern: "*.genome.bam"
- bam_transcript:
type: file
description: Transcript BAM file (optional)
pattern: "*.transcript.bam"
authors:
- "@drpatelh"
- "@kevinmenden"