mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +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>
52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: ivar_trim
|
|
description: Trim primer sequences rom a BAM file with iVar
|
|
keywords:
|
|
- amplicon sequencing
|
|
- trimming
|
|
- fasta
|
|
tools:
|
|
- ivar:
|
|
description: |
|
|
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
|
|
homepage: https://github.com/andersen-lab/ivar
|
|
documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
|
|
licence: ["GPL-3.0-or-later"]
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: Co-ordinate sorted BAM file
|
|
pattern: "*.bam"
|
|
- bai:
|
|
type: file
|
|
description: Index file for co-ordinate sorted BAM file
|
|
pattern: "*.bai"
|
|
- bed:
|
|
type: file
|
|
description: BED file with primer labels and positions
|
|
pattern: "*.bed"
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: iVar generated trimmed bam file (unsorted)
|
|
pattern: "*.bam"
|
|
- log:
|
|
type: file
|
|
description: Log file generated by iVar for use with MultiQC
|
|
pattern: "*.log"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@andersgs"
|
|
- "@drpatelh"
|