nf-core_modules/modules/fgbio/fastqtobam/meta.yml
Francesco L a0bc08732c
Rewritten module fgbio/fastqtobam (#916)
* added template for fastqtobam

* porting old code into new template

* update with missing getprocessname function

* test completed - updating all

* fixed linting issues

* improved reading

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 19:06:06 +02:00

47 lines
1.7 KiB
YAML

name: fgbio_fastqtobam
description: |
Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file
keywords:
- fastqtobam
- fgbio
tools:
- fgbio:
description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
homepage: http://fulcrumgenomics.github.io/fgbio/
documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
tool_dev_url: https://github.com/fulcrumgenomics/fgbio
doi: ""
licence: ['MIT']
input:
- reads:
type: file
description: pair of reads to be converted into BAM file
pattern: "*.{fastq.gz}"
- read_structure:
type: string
description: |
A read structure should always be provided for each of the fastq files.
If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string
will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T").
If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "*.{version.yml}"
- umibam:
type: file
description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any)
pattern: "*.{bam}"
authors:
- "@lescai"