nf-core_modules/modules/samtools/collatefastq/meta.yml
Maxime U. Garcia 705f8c9ac4
Add samtools/collatefastq module (#1536)
* add samtools/collatefastq module

* update yml file

* improve output
2022-04-20 10:05:17 +02:00

48 lines
1.2 KiB
YAML

name: samtools_collatefastq
description: |
The module uses collate and then fastq methods from samtools to
convert a SAM, BAM or CRAM file to FASTQ format
keywords:
- bam2fq
- samtools
- fastq
tools:
- samtools:
description: Tools for dealing with SAM, BAM and CRAM files
homepage: None
documentation: http://www.htslib.org/doc/1.1/samtools.html
tool_dev_url: None
doi: ""
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}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
or a single interleaved .fq.gz file if the user chooses not to split the reads.
pattern: "*.fq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@lescai"
- "@maxulysse"