mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 23:49:55 +00:00
79 lines
2.2 KiB
YAML
Generated
79 lines
2.2 KiB
YAML
Generated
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"
|