nf-core_modules/software/star/align/meta.yml

98 lines
2.8 KiB
YAML
Raw Normal View History

name: star_align
description: Align reads to a reference genome using STAR
keywords:
- align
- fasta
- genome
- reference
tools:
- star:
description: |
STAR is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: https://github.com/alexdobin/STAR
manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
doi: 10.1093/bioinformatics/bts635
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: directory
description: STAR genome index
pattern: "star"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- log_final:
type: file
description: STAR final log file
pattern: "*Log.final.out"
- log_out:
type: file
description: STAR lot out file
pattern: "*Log.out"
- log_progress:
type: file
description: STAR log progress file
pattern: "*Log.progress.out"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
2021-01-26 12:31:30 +00:00
- bam_sorted:
type: file
description: Sorted BAM file of read alignments (optional)
pattern: "*sortedByCoord.out.bam"
- bam_transcript:
type: file
description: Output BAM file of transcriptome alignment (optional)
pattern: "*toTranscriptome.out.bam"
- bam_unsorted:
type: file
description: Unsorted BAM file of read alignments (optional)
pattern: "*Aligned.unsort.out.bam"
- fastq:
type: file
description: Unmapped FastQ files (optional)
pattern: "*fastq.gz"
- tab:
type: file
description: STAR output tab file(s) (optional)
pattern: "*.tab"
authors:
- "@kevinmenden"
- "@drpatelh"