mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
36049bf544
* fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
43 lines
1.2 KiB
YAML
43 lines
1.2 KiB
YAML
name: fgbio_fastqtobam
|
|
description: |
|
|
Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
|
|
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}"
|
|
|
|
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}"
|
|
- bam:
|
|
type: file
|
|
description: Unaligned, unsorted BAM file
|
|
pattern: "*.{bam}"
|
|
- cram:
|
|
type: file
|
|
description: Unaligned, unsorted CRAM file
|
|
pattern: "*.{cram}"
|
|
|
|
authors:
|
|
- "@lescai"
|
|
- "@matthdsm"
|