2021-01-25 14:14:57 +00:00
|
|
|
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
|
|
|
|
|
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"
|
2021-01-25 14:14:57 +00:00
|
|
|
|
|
|
|
|
authors:
|
|
|
|
|
- "@kevinmenden"
|
|
|
|
|
- "@drpatelh"
|
