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meta.yml
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meta.yml
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name: samtools_collatefastq
description: |
The module uses collate and then fastq methods from samtools to
convert a SAM, BAM or CRAM file to FASTQ format
keywords:
- bam2fq
- samtools
- fastq
tools:
- samtools:
description: Tools for dealing with SAM, BAM and CRAM files
documentation: http://www.htslib.org/doc/1.1/samtools.html
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}"
- meta2:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'test' ]
- fasta:
type: file
description: Reference genome fasta file
pattern: "*.{fasta,fa}"
- interleave:
type: boolean
description: |
If true, the output is a single interleaved paired-end FASTQ
If false, the output split paired-end FASTQ
default: false
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastq:
type: file
description: |
R1 and R2 FASTQ files
pattern: "*_{1,2}.fq.gz"
- fastq_interleaved:
type: file
description: |
Interleaved paired end FASTQ files
pattern: "*_interleaved.fq.gz"
- fastq_other:
type: file
description: |
FASTQ files with reads where the READ1 and READ2 FLAG bits set are either both set or both unset.
pattern: "*_other.fq.gz"
- fastq_singleton:
type: file
description: |
FASTQ files with singleton reads.
pattern: "*_singleton.fq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@lescai"
- "@maxulysse"
- "@matthdsm"
maintainers:
- "@lescai"
- "@maxulysse"
- "@matthdsm"