mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-27 14:29:55 +00:00
62 lines
1.9 KiB
YAML
Generated
62 lines
1.9 KiB
YAML
Generated
name: samtools_fastq
|
|
description: Converts a SAM/BAM/CRAM file to FASTQ
|
|
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: http://www.htslib.org/doc/samtools.html
|
|
doi: 10.1093/bioinformatics/btp352
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- input:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- interleave:
|
|
type: boolean
|
|
description: Set true for interleaved fastq file
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- fastq:
|
|
type: file
|
|
description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
|
|
pattern: "*_{1,2}.fastq.gz"
|
|
- interleaved:
|
|
type: file
|
|
description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
|
|
pattern: "*_interleaved.fastq.gz"
|
|
- singleton:
|
|
type: file
|
|
description: Compressed FASTQ file with singleton reads
|
|
pattern: "*_singleton.fastq.gz"
|
|
- other:
|
|
type: file
|
|
description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
|
|
pattern: "*_other.fastq.gz"
|
|
|
|
authors:
|
|
- "@priyanka-surana"
|
|
- "@suzannejin"
|