mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +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>
58 lines
1.9 KiB
YAML
58 lines
1.9 KiB
YAML
name: bamcmp
|
|
description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
|
|
keywords:
|
|
- filter
|
|
- xenograft
|
|
- host
|
|
- graft
|
|
- contamination
|
|
- mouse
|
|
|
|
tools:
|
|
- bamcmp:
|
|
description:
|
|
Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
|
|
sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
|
|
reads which multimap to the contamination genome will be spuriously kept.
|
|
homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
|
|
documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
|
|
tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
|
|
doi: "10.1158/1541-7786.MCR-16-0431"
|
|
licence: ["GPL v3"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test']
|
|
|
|
- sample:
|
|
type: file
|
|
description: BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
- contaminant:
|
|
type: file
|
|
description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
output:
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
- bam:
|
|
type: file
|
|
description: Bam file containing the reads which align better to the primary genome.
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
- bam:
|
|
type: file
|
|
description: Bam file containing the reads which align better to the contaminant genome.
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
authors:
|
|
- "@kmurat1"
|
|
- "@sppearce"
|