mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +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>
47 lines
1.3 KiB
YAML
47 lines
1.3 KiB
YAML
name: umitools_extract
|
|
description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
|
|
keywords:
|
|
- umitools
|
|
- extract
|
|
tools:
|
|
- umi_tools:
|
|
description: >
|
|
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
|
|
and single cell RNA-Seq cell barcodes
|
|
documentation: https://umi-tools.readthedocs.io/en/latest/
|
|
license: ["MIT"]
|
|
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 whose UMIs will be extracted.
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: >
|
|
Extracted FASTQ files. |
|
|
For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
|
|
For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
|
|
pattern: "*.{fastq.gz}"
|
|
- log:
|
|
type: file
|
|
description: Logfile for umi_tools
|
|
pattern: "*.{log}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@drpatelh"
|
|
- "@grst"
|