mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
55 lines
1.7 KiB
YAML
55 lines
1.7 KiB
YAML
|
name: cat_fastq
|
||
|
|
description: Concatenates fastq files
|
||
|
|
keywords:
|
||
|
|
- fastq
|
||
|
|
- concatenate
|
||
|
|
tools:
|
||
|
|
- cat:
|
||
|
|
description: |
|
||
|
|
The cat utility reads files sequentially, writing them to the standard output.
|
||
|
|
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
|
||
|
|
params:
|
||
|
|
- outdir:
|
||
|
|
type: string
|
||
|
|
description: |
|
||
|
|
The pipeline's output directory. By default, the module will
|
||
|
|
output files into `$params.outdir/<SOFTWARE>`
|
||
|
|
- publish_dir_mode:
|
||
|
|
type: string
|
||
|
|
description: |
|
||
|
|
Value for the Nextflow `publishDir` mode parameter.
|
||
|
|
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
||
|
|
- enable_conda:
|
||
|
|
type: boolean
|
||
|
|
description: |
|
||
|
|
Run the module with Conda using the software specified
|
||
|
|
via the `conda` directive
|
||
|
|
- singularity_pull_docker_container:
|
||
|
|
type: boolean
|
||
|
|
description: |
|
||
|
|
Instead of directly downloading Singularity images for use with Singularity,
|
||
|
|
force the workflow to pull and convert Docker containers instead.
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- reads:
|
||
|
|
type: list
|
||
|
|
description: |
|
||
|
|
List of input FastQ files to be concatenated.
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- reads:
|
||
|
|
type: file
|
||
|
|
description: Merged fastq file
|
||
|
|
pattern: "*.{merged.fastq.gz}"
|
||
|
|
authors:
|
||
|
|
- "@joseespinosa"
|
||
|
|
- "@drpatelh"
|