modules/bam2fastx_bam2fastq

Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data

bam2fastxbam2fastqpacbio

https://github.com/nf-core/modules/[...]/modules/nf-core/bam2fastx/bam2fastq

Description

Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data

Input

name:type

description

pattern

`meta:map`

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

]

`bam:file`

PacBio BAM file

*.bam

`index:file`

PacBio BAM file index (.pbi)

*.pbi

Output

name:type

description

pattern

`fastq`

`meta:map`

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

]

`*.fastq.gz:file`

Gzipped FASTQ file

*.fastq.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

bam2fastx
BSD-3-clause-Clear

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files

github.com/PacificBiosciences/bam2fastx

modules/bam2fastx_bam2fastq

Description

Input

`meta:map`

`bam:file`

`index:file`

Output

`fastq`

`meta:map`

`*.fastq.gz:file`

`versions`

`versions.yml:file`

Tools

bam2fastx
BSD-3-clause-Clear

maintainers

get in touch

modules/bam2fastx_bam2fastq

Description

Input

meta:map

bam:file

index:file

Output

fastq

meta:map

*.fastq.gz:file

versions

versions.yml:file

Tools

bam2fastx BSD-3-clause-Clear

maintainers

get in touch

`meta:map`

`bam:file`

`index:file`

`fastq`

`meta:map`

`*.fastq.gz:file`

`versions`

`versions.yml:file`

bam2fastx
BSD-3-clause-Clear