mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
879d42c5e2
* refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings
90 lines
3 KiB
YAML
90 lines
3 KiB
YAML
name: adapterremoval
|
|
description: Trim sequencing adapters and collapse overlapping reads
|
|
keywords:
|
|
- trimming
|
|
- adapters
|
|
- merging
|
|
- fastq
|
|
tools:
|
|
- adapterremoval:
|
|
description: The AdapterRemoval v2 tool for merging and clipping reads.
|
|
homepage: https://github.com/MikkelSchubert/adapterremoval
|
|
documentation: https://adapterremoval.readthedocs.io
|
|
licence: ["GPL v3"]
|
|
|
|
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.
|
|
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
|
|
- adapterlist:
|
|
type: file
|
|
description: Optional text file containing list of adapters to look for for removal
|
|
with one adapter per line. Otherwise will look for default adapters (see
|
|
AdapterRemoval man page), or can be modified to remove user-specified
|
|
adapters via ext.args.
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- singles_truncated:
|
|
type: file
|
|
description: |
|
|
Adapter trimmed FastQ files of either single-end reads, or singleton
|
|
'orphaned' reads from merging of paired-end data (i.e., one of the pair
|
|
was lost due to filtering thresholds).
|
|
pattern: "*.truncated.fastq.gz"
|
|
- discarded:
|
|
type: file
|
|
description: |
|
|
Adapter trimmed FastQ files of reads that did not pass filtering
|
|
thresholds.
|
|
pattern: "*.discarded.fastq.gz"
|
|
- pair1_truncated:
|
|
type: file
|
|
description: |
|
|
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
|
|
with their respective R2 pair due to long templates. The respective pair
|
|
is stored in 'pair2_truncated'.
|
|
pattern: "*.pair1.truncated.fastq.gz"
|
|
- pair2_truncated:
|
|
type: file
|
|
description: |
|
|
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
|
|
with their respective R1 pair due to long templates. The respective pair
|
|
is stored in 'pair1_truncated'.
|
|
pattern: "*.pair2.truncated.fastq.gz"
|
|
- collapsed:
|
|
type: file
|
|
description: |
|
|
Collapsed FastQ of paired-end reads that successfully merged with their
|
|
respective R1 pair but were not trimmed.
|
|
pattern: "*.collapsed.fastq.gz"
|
|
- collapsed_truncated:
|
|
type: file
|
|
description: |
|
|
Collapsed FastQ of paired-end reads that successfully merged with their
|
|
respective R1 pair and were trimmed of adapter due to sufficient overlap.
|
|
pattern: "*.collapsed.truncated.fastq.gz"
|
|
- log:
|
|
type: file
|
|
description: AdapterRemoval log file
|
|
pattern: "*.settings"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@maxibor"
|
|
- "@jfy133"
|