nf-core_modules/modules/samtools/ampliconclip/meta.yml

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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 ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- 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"