nf-core_modules/modules/rsem/calculateexpression/meta.yml
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00

63 lines
1.7 KiB
YAML

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
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"
- version:
type: file
description: File containing software version
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"