mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 16:12:04 +00:00
2e619add87
* created template for `samtools/ampliconclip` (#584) * All tests passing (#584) * Linting fixed (#584) * Final linting fixed (#584) * Optional output flags moved to `input` (#584) * typo fix (#584) * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
64 lines
1.7 KiB
YAML
64 lines
1.7 KiB
YAML
name: samtools_ampliconclip
|
|
description: write your description here
|
|
keywords:
|
|
- amplicon
|
|
- clipping
|
|
- ampliconclip
|
|
- samtools ampliconclip
|
|
- samtools
|
|
tools:
|
|
- samtools:
|
|
description: |
|
|
SAMtools is a set of utilities for interacting with and post-processing
|
|
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
|
|
These files are generated as output by short read aligners like BWA.
|
|
homepage: http://www.htslib.org/
|
|
documentation: hhttp://www.htslib.org/doc/samtools.html
|
|
doi: 10.1093/bioinformatics/btp352
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- bed:
|
|
type: file
|
|
description: BED file of regions to be removed (e.g. amplicon primers)
|
|
pattern: "*.{bed}"
|
|
- save_cliprejects:
|
|
type: value
|
|
description: Save filtered reads to a file
|
|
- save_clipstats:
|
|
type: value
|
|
description: Save clipping stats to a file
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
- bam:
|
|
type: file
|
|
description: Clipped reads BAM file
|
|
pattern: "*.{bam}"
|
|
- stats:
|
|
type: file
|
|
description: Clipping statistics text file
|
|
pattern: "*.{clipstats.txt}"
|
|
- rejects_bam:
|
|
type: file
|
|
description: Filtered reads BAM file
|
|
pattern: "*.{cliprejects.bam}"
|
|
|
|
authors:
|
|
- "@bjohnnyd"
|