mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
ee46c19d03
* add Picard FastqToSam * Update test.yml * update tests * possible fix? * fixed! * Update modules/picard/fastqtosam/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Update modules/picard/fastqtosam/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * simplify tests * fix tests * revert version check Co-authored-by: CMGG ICT Team <ict@cmgg.be> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
46 lines
1.2 KiB
YAML
46 lines
1.2 KiB
YAML
name: "picard_fastqtosam"
|
|
description: Converts a FASTQ file to an unaligned BAM or SAM file.
|
|
keywords:
|
|
- fastq
|
|
- unaligned
|
|
- bam
|
|
tools:
|
|
- picard:
|
|
description: |
|
|
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
|
|
data and formats such as SAM/BAM/CRAM and VCF.
|
|
homepage: https://broadinstitute.github.io/picard/
|
|
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard-
|
|
tool_dev_url: https://github.com/broadinstitute/picard
|
|
licence: ["MIT"]
|
|
|
|
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.
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
#
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- bam:
|
|
type: file
|
|
description: Unaligned bam file
|
|
pattern: "*.{bam}"
|
|
|
|
authors:
|
|
- "@matthdsm"
|