2021-03-23 11:13:07 +00:00
|
|
|
name: samtools_fastq
|
2021-03-23 17:43:52 +00:00
|
|
|
description: Converts a SAM/BAM/CRAM file to FASTQ
|
2021-03-23 11:13:07 +00:00
|
|
|
keywords:
|
|
|
|
- bam
|
|
|
|
- sam
|
|
|
|
- cram
|
|
|
|
- fastq
|
|
|
|
tools:
|
|
|
|
- samtools:
|
|
|
|
description: |
|
|
|
|
SAMtools is a set of utilities for interacting with and post-processing
|
|
|
|
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
|
|
|
|
These files are generated as output by short read aligners like BWA.
|
|
|
|
homepage: http://www.htslib.org/
|
|
|
|
documentation: hhttp://www.htslib.org/doc/samtools.html
|
|
|
|
doi: 10.1093/bioinformatics/btp352
|
2021-10-22 22:39:54 +00:00
|
|
|
licence: ['MIT']
|
2021-03-23 11:13:07 +00:00
|
|
|
input:
|
|
|
|
- meta:
|
|
|
|
type: map
|
|
|
|
description: |
|
|
|
|
Groovy Map containing sample information
|
|
|
|
e.g. [ id:'test', single_end:false ]
|
|
|
|
- bam:
|
|
|
|
type: file
|
|
|
|
description: BAM/CRAM/SAM file
|
|
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
output:
|
|
|
|
- meta:
|
|
|
|
type: map
|
|
|
|
description: |
|
|
|
|
Groovy Map containing sample information
|
|
|
|
e.g. [ id:'test', single_end:false ]
|
2022-02-14 10:02:03 +00:00
|
|
|
- fastq:
|
2021-03-23 11:13:07 +00:00
|
|
|
type: file
|
2021-03-23 17:43:52 +00:00
|
|
|
description: compressed FASTQ file
|
|
|
|
pattern: "*.fastq.gz"
|
2021-10-03 07:20:26 +00:00
|
|
|
- versions:
|
2021-03-23 11:13:07 +00:00
|
|
|
type: file
|
2021-10-03 07:20:26 +00:00
|
|
|
description: File containing software versions
|
2021-09-27 08:41:24 +00:00
|
|
|
pattern: "versions.yml"
|
2021-03-23 11:13:07 +00:00
|
|
|
authors:
|
|
|
|
- "@suzannejin"
|