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taxprofiler/modules/nf-core/samtools/view/meta.yml
2022-10-05 12:24:18 +02:00

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name: samtools_view
description: filter/convert SAM/BAM/CRAM file
keywords:
- view
- bam
- sam
- cram
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
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- index:
type: optional file
description: BAM.BAI/CRAM.CRAI file
pattern: "*.{.bai,.crai}"
- fasta:
type: optional file
description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}"
- qname:
type: file
description: Optional file with read names to output only select alignments
pattern: "*.{txt,list}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: optional filtered/converted BAM file
pattern: "*.{bam}"
- cram:
type: file
description: optional filtered/converted CRAM file
pattern: "*.{cram}"
- sam:
type: file
description: optional filtered/converted SAM file
pattern: "*.{sam}"
# bai, csi, and crai are created with `--write-index`
- bai:
type: file
description: optional BAM file index
pattern: "*.{bai}"
- csi:
type: file
description: optional tabix BAM file index
pattern: "*.{csi}"
- crai:
type: file
description: optional CRAM file index
pattern: "*.{crai}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@joseespinosa"
- "@FriederikeHanssen"
- "@priyanka-surana"