mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
64 lines
1.7 KiB
YAML
64 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
|
|
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"
|