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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>
44 lines
1.3 KiB
YAML
44 lines
1.3 KiB
YAML
name: samtools_depth
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description: Computes the depth at each position or region.
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keywords:
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- depth
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- samtools
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- statistics
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- coverage
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tools:
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- samtools:
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description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region
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homepage: http://www.htslib.org
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documentation: http://www.htslib.org/doc/samtools-depth.html
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tool_dev_url: https://github.com/samtools/samtools
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doi: "10.1093/bioinformatics/btp352"
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: sorted BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- tsv:
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type: file
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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
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pattern: "*.{tsv}"
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authors:
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- "@louperelo"
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