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:false ]

`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:false ]

`*.fastq.gz`
`:file`

Gzipped FASTQ file

*.fastq.gz

`versions_bam2fastx`

`${task.process}`
`:string`

The name of the process

`bam2fastx`
`:string`

The name of the tool

`bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`bam2fastx`
`:string`

The name of the tool

`bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'`
`:eval`

The expression to obtain the version of the tool

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_bam2fastx`

`${task.process}`
`:string`

`bam2fastx`
`:string`

`bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`bam2fastx`
`:string`

`bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'`
`:eval`

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_bam2fastx

${task.process}:string

bam2fastx:string

bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //':eval

Topics

versions

${task.process}:string

bam2fastx:string

bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //':eval

Tools

bam2fastx BSD-3-clause-Clear

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`index`
`:file`

`fastq`

`meta`
`:map`

`*.fastq.gz`
`:file`

`versions_bam2fastx`

`${task.process}`
`:string`

`bam2fastx`
`:string`

`bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'`
`:eval`

`versions`

`${task.process}`
`:string`

`bam2fastx`
`:string`

`bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'`
`:eval`

bam2fastx
BSD-3-clause-Clear