modules/samtools_collatefastq

The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format

bam2fqsamtoolsfastq

https://github.com/nf-core/modules/[...]/modules/nf-core/samtools/collatefastq

Description

The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`input:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`meta2:map`

Groovy Map containing reference information e.g. [ id:‘test’ ]

`fasta:file`

Reference genome fasta file

*.{fasta,fa}

`interleave:boolean`

If true, the output is a single interleaved paired-end FASTQ If false, the output split paired-end FASTQ

Output

name:type

description

pattern

`fastq`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_{1,2}.fq.gz

`*_{1,2}.fq.gz:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_{1,2}.fq.gz

`fastq_interleaved`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_interleaved.fq.gz

`*_interleaved.fq:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_interleaved.fq.gz

`fastq_other`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_other.fq.gz

`*_other.fq.gz:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_other.fq.gz

`fastq_singleton`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_singleton.fq.gz

`*_singleton.fq.gz:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_singleton.fq.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

samtools
MIT

Tools for dealing with SAM, BAM and CRAM files

http://www.htslib.org/doc/1.1/samtools

modules/samtools_collatefastq

Description

Input

meta:map

input:file

meta2:map

fasta:file

interleave:boolean

Output

fastq

meta:map

*_{1,2}.fq.gz:map

fastq_interleaved

meta:map

*_interleaved.fq:map

fastq_other

meta:map

*_other.fq.gz:map

fastq_singleton

meta:map

*_singleton.fq.gz:map

versions

versions.yml:file

Tools

samtools MIT

`meta:map`

`input:file`

`meta2:map`

`fasta:file`

`interleave:boolean`

`fastq`

`meta:map`

`*_{1,2}.fq.gz:map`

`fastq_interleaved`

`meta:map`

`*_interleaved.fq:map`

`fastq_other`

`meta:map`

`*_other.fq.gz:map`

`fastq_singleton`

`meta:map`

`*_singleton.fq.gz:map`

`versions`

`versions.yml:file`

samtools
MIT