mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 13:23:09 +00:00
53109d53c0
* Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.4 KiB
YAML
47 lines
1.4 KiB
YAML
name: gatk4_fastqtosam
|
|
description: Converts FastQ file to BAM format
|
|
keywords:
|
|
- bam
|
|
- fastq
|
|
- convert
|
|
tools:
|
|
- gatk4:
|
|
description: Genome Analysis Toolkit (GATK4)
|
|
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
|
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
|
and high-performance computing features make it capable of taking on projects of any size.
|
|
homepage: https://gatk.broadinstitute.org/hc/en-us
|
|
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
|
|
tool_dev_url: https://github.com/broadinstitute/gatk
|
|
doi: "10.1158/1538-7445.AM2017-3590"
|
|
licence: ['BSD-3-clause']
|
|
|
|
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: "*.fastq.gz"
|
|
|
|
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.txt}"
|
|
- bam:
|
|
type: file
|
|
description: Converted BAM file
|
|
pattern: "*.bam"
|
|
|
|
authors:
|
|
- "@ntoda03"
|