mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: samtools_bam2fq
|
|
description: |
|
|
The module uses bam2fq method 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 ]
|
|
- inputbam:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- split:
|
|
type: boolean
|
|
description: |
|
|
TRUE/FALSE value to indicate if reads should be separated into
|
|
/1, /2 and if present other, or singleton.
|
|
Note: choosing TRUE will generate 4 different files.
|
|
Choosing FALSE will produce a single file, which will be interleaved in case
|
|
the input contains paired reads.
|
|
|
|
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"
|
|
- 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"
|
|
|
|
authors:
|
|
- "@lescai"
|