nf-core_modules/modules/rsem/calculateexpression/meta.yml
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

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* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +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: "*.{version.txt}"
- 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"