nf-core_modules/modules/samtools/depth/meta.yml
Matthias Hörtenhuber e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* 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>
2022-02-15 11:15:27 +00:00

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name: samtools_depth
description: Computes the depth at each position or region.
keywords:
- depth
- samtools
- statistics
- coverage
tools:
- samtools:
description: Tools for dealing with SAM, BAM and CRAM files; samtools depth computes the read depth at each position or region
homepage: http://www.htslib.org
documentation: http://www.htslib.org/doc/samtools-depth.html
tool_dev_url: https://github.com/samtools/samtools
doi: "10.1093/bioinformatics/btp352"
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: sorted BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
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"
- tsv:
type: file
description: The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position
pattern: "*.{tsv}"
authors:
- "@louperelo"