mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
99 lines
3.4 KiB
YAML
99 lines
3.4 KiB
YAML
name: trimgalore
|
|
description: Trim FastQ files using Trim Galore!
|
|
keywords:
|
|
- trimming
|
|
- adapters
|
|
- sequencing adapters
|
|
- fastq
|
|
tools:
|
|
- trimgalore:
|
|
description: |
|
|
A wrapper tool around Cutadapt and FastQC to consistently apply quality
|
|
and adapter trimming to FastQ files, with some extra functionality for
|
|
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
|
|
homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
|
documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
|
|
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.
|
|
- clip_r1:
|
|
type: integer
|
|
description: |
|
|
Instructs Trim Galore to remove bp from the 5' end of read 1
|
|
(or single-end reads)
|
|
- clip_r2:
|
|
type: integer
|
|
description: |
|
|
Instructs Trim Galore to remove bp from the 5' end of read 2
|
|
(paired-end reads only)
|
|
- three_prime_clip_r1:
|
|
type: integer
|
|
description: |
|
|
Instructs Trim Galore to remove bp from the 3' end of read 1
|
|
AFTER adapter/quality trimming has been performed
|
|
- three_prime_clip_r2:
|
|
type: integer
|
|
description: |
|
|
Instructs Trim Galore to re move bp from the 3' end of read 2
|
|
AFTER adapter/quality trimming has been performed
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
List of input adapter trimmed FastQ files of size 1 and 2 for
|
|
single-end and paired-end data, respectively.
|
|
pattern: "*.{fq.gz}"
|
|
- html:
|
|
type: file
|
|
description: FastQC report (optional)
|
|
pattern: "*_{fastqc.html}"
|
|
- zip:
|
|
type: file
|
|
description: FastQC report archive (optional)
|
|
pattern: "*_{fastqc.zip}"
|
|
- log:
|
|
type: file
|
|
description: Trim Galore! trimming report
|
|
pattern: "*_{report.txt}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@drpatelh"
|
|
- "@ewels"
|
|
- "@FelixKrueger"
|