nf-core_modules/software/trimgalore/meta.yml

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name: trimgalore
description: Trim FastQ files using Trim Galore!
keywords:
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- trimming
- adapters
- sequencing adapters
- fastq
tools:
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- 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
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params:
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- 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.
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- enable_conda:
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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.
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- 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:
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- 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:
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- 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:
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- "@drpatelh"
- "@ewels"
- "@FelixKrueger"