mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +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>
50 lines
1.7 KiB
YAML
Executable file
50 lines
1.7 KiB
YAML
Executable file
name: sequenzautils_bam2seqz
|
|
description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
|
|
keywords:
|
|
- bam2seqz
|
|
tools:
|
|
- sequenzautils:
|
|
description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
|
|
homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html
|
|
documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html
|
|
doi: 10.1093/annonc/mdu479
|
|
licence: ["GPL-3.0-or-later"]
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- normalbam:
|
|
type: file
|
|
description: BAM file from the reference/normal sample
|
|
pattern: "*.{bam}"
|
|
- tumourbam:
|
|
type: file
|
|
description: BAM file from the tumour sample
|
|
pattern: "*.{bam}"
|
|
- fasta:
|
|
type: file
|
|
description: Reference FASTA file
|
|
pattern: "*.{fasta}"
|
|
- wigfile:
|
|
type: file
|
|
description: GC content wiggle file
|
|
pattern: "*.{wig.gz}"
|
|
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"
|
|
- seqz:
|
|
type: file
|
|
description: Seqz file
|
|
pattern: "*.{seqz.gz}"
|
|
|
|
authors:
|
|
- "@kaurravneet4123"
|